Wow! I don't really understand why you have your setup with a motherboard audio devise but I really think you should at least try running "recording" without the onboard. That is the problem... I think you need to decide if you want great recording or some other obscure setup. just saying, with all respect. :) you can always reinstall the onboard audio. Good luck :) 
If I think of anything else I'll et you know.
 
peace!
 

11Dreams
Wow! I don't really understand why you have your setup with a motherboard audio devise but I really think you should at least try running "recording" without the onboard. That is the problem... I think you need to decide if you want great recording or some other obscure setup. just saying, with all respect. :) you can always reinstall the onboard audio. Good luck :) 
If I think of anything else I'll et you know.
 
peace!
 

Thanks for your advice. I think I may try uninstalling the Realtec and see if that makes any difference.
 
I've been using onboard audio for playing mp3's and wav files for many years with another sound card and Win 7 also. Jim Roseberry built this computer and actually has the AVB card too.
 
He thought it was fine to use the onboard audio for Win Media. Yet I think it's a worthwhile experiment to see if it eliminates the crackles. Sometimes I will play an mp3 with Win Media player and set the tempo in Sonar in real time
 

Another obscure problem I had with recording with the MOTU was while having "remove DC offset" enabled in Sonar's preferences. It would cause some weird low level crackles on mono tracks all the time. Unchecking "remove DC offset" fixed that problem. Someone from Cakewalk emailed me back and confirmed that was actually an ongoing Sonar bug. You could check your preferences.

Have you updated the unit to latest drivers and firmware?  There may have been a windows update that pooched something if you are using older drivers and firmware.

ryecatchermark
Another obscure problem I had with recording with the MOTU was while having "remove DC offset" enabled in Sonar's preferences. It would cause some weird low level crackles on mono tracks all the time. Unchecking "remove DC offset" fixed that problem. Someone from Cakewalk emailed me back and confirmed that was actually an ongoing Sonar bug. You could check your preferences.

yes I have remove DC offset during record unchecked. This permanently recording the crackles is pretty intermittent. I've been doing a crackle test every day for 3 weeks. And the last crackle happened 10 days later. I have the latest firmware and software.

History: I did have a few problems like that back in 2015 with the 1248 and Windows 7.  The firmware update that came out mid summer 15 took care of it.  I then updated to a new machine and Windows 10..  I did get crackles on recording but it was tied to disk usage - and the culprit was antivirus scans, and a few Windows supplied tools that I tuned off.  The windows 10, current MOTU driver, current DAW updates strategy worked flawlessly until about 5 weeks ago.  
 
First - I do not know the culprit BUT I suspect it to be in the WUP sequence of events.  I have tested this at least 3 times.  Turn on the machine, bring up the DAW, then test record.  If I got a crackle in test, I closed out the DAW, and re-booted.  Bring up the DAW, crackling gone.  Every time.   I cannot tell if the sequence is  WUP before install crackles, WUP during install crackles, or WUP and crackles after update, before boot - if that makes any sense.
 
Second - It seems to be happening the same way with my Presonus RM32ai interface, at least it happened a few nights ago.
 
Again - my single observations SEEMS tied to WUP to me.  I can assure you it could be tied to disk usage too.       
 
 

LLyons
History: I did have a few problems like that back in 2015 with the 1248 and Windows 7.  The firmware update that came out mid summer 15 took care of it.  I then updated to a new machine and Windows 10..  I did get crackles on recording but it was tied to disk usage - and the culprit was antivirus scans, and a few Windows supplied tools that I tuned off.  The windows 10, current MOTU driver, current DAW updates strategy worked flawlessly until about 5 weeks ago.  
 
First - I do not know the culprit BUT I suspect it to be in the WUP sequence of events.  I have tested this at least 3 times.  Turn on the machine, bring up the DAW, then test record.  If I got a crackle in test, I closed out the DAW, and re-booted.  Bring up the DAW, crackling gone.  Every time.   I cannot tell if the sequence is  WUP before install crackles, WUP during install crackles, or WUP and crackles after update, before boot - if that makes any sense.
 
Second - It seems to be happening the same way with my Presonus RM32ai interface, at least it happened a few nights ago.
 
Again - my single observations SEEMS tied to WUP to me.  I can assure you it could be tied to disk usage too.       
 
 

I saw a Sonar post about a recent WUP, possibly even the current one, causing some problems. I've been leery of using WUP until I know what's going on with that.
 
As for me I tend to do the WUP right before I install a new Plat version. Since I'm using currently 2017.04 I haven't had any WUP in a while. Unless MS has done some secret updates like they did last year that messed some of us up.
 
Has the most current WUP helped what happened 5 weeks ago? What Win  tools have you disabled?

1) Definitely use the latest drivers. MOTU made quite some changes which affected performance.

2) remember you need to set buffer settings so that they fit your system i.e. try not just with different values for the main ASIO buffer but adjust the host safety accordingly. If using direct monitoring via MOTU mixer you can use large buffers. Increase the host safety accordingly. One of the mistakes i made was being lazy and keeping it at 32 while just setting the main value higher or lower.

3) try a different USB port and/or unplug other USB devices. If you do not know how your ports are feeding into which USB root download a free software which will list what goes where internally. I had a problem that the A-PRO MIDI controller caused some audio crackles, discovered it by plugging USB cables to different ports. Reinstalling the A-PRO driver fixed it. Since everything had worked fine before I strongly suspect a Windows update causing the problem in my case!

Good hearing from you Rob, I remember we had some good discussion s about MOTU before. I’m using the latest drivers and firmware from MOTU. I raised my buffers recently to help this problem. I’m now using 256 256. Since I’m a keyboard player, I don’t want to set the latency too high or it’ll make it hard to play with good timing. Shouldn’t that be good enough?
 
This crackle problem I have occurs with very low load -  a few audio tracks and midi tracks, not much FX. IN fact my basic crackle test has no audio or midi (except drum loops). I sometimes get crackles with it and no load.
 
I just changed the USB port for the AVB. I’m using a USB 2.0 port. I think MOTU said 3.0 won’t help any. I did disconnect a 2T USB HD that is my wav file archive HD for all my songs. Let’s see if any of that makes a difference.
 
Can you tell me what free software which will list what USB goes where internally? Not sure if this is what you’re asking, but I think my USB ports are in pairs, which are linked in some way. I do have lots of USB stuff plugged in – 2 dongles, wireless keyboard, backup HD, 2 printers, midi interface. My computer is 2.5 years old and is a Jim Roseberry DAW

I agree with Rob's statement about the USB ports.  I had crackles and bad performance when I first got my MotU.  I had all my music stuff plugged into a USB card.  Moving to a USB port directly on the MB made all the difference in the world.  If you have a Jim Roseberry DAW, you might contact him for some tech support on the USB ports.  I think he offers lifetime support (or ping him in the hardware section - he doesn't venture up here much.)