Guys I hope you can help me out or give me ideas on where to look, let me know if you have ever experienced this...
 
Equipment chain at input:
multiple different mic's  (seems to happen randomly sometimes while tracking drums, others just a vocal and anything in between)
cables, a 16 channel snake
My Presonus 24.4.2
Firewire'd into my computer (ADK)
Sonar X3 Producer
 
I have a few songs that I have recorded for bands/or 1 I did on my own that I didn't notice during capture but later on playback that I am getting a pop noise (almost what you would expect to hear if a drummer hit your 57 with a stick by accident) but it will be in the same spot & and on every track that was being recorded simultaneously at that time.  To get rid of it I am having to go and zoom WAAAY in and cross fade out and back in after it, on every track.  2 kick mics, 2 snares, 3 toms, hats, ride, overheads, and room mics....  I have had it happen while tracking vocals, and bass too.  I am running X3 in 64 bit.  This is the 1st time I have run my DAW in 64 as I was a staying in the 32 bit realm before.   While recording I can see the little CPU gauge in sonar and I am barely registering anything at all in usage during tracking yet I can't help but think this seems like a CPU hiccup or a glitch in X3 as this gear worked flawlessly in X2 32 bit.     Has anyone dealt with this before?

by the way,   My system has an intel i3 540 @ 3.07 ghz, 4 GB Ram, 2 Seagate 500 drives.  My OS drive has maybe 15% used/full, and my audio drive has about 8% used/full

Hi, Chuck. Yeah, sounds like a dropout. As far as I know with 4GB of RAM there is no benefit of running a 64bit OS or programs. 64bit is (again as far as I know) designed to take advantage of more than 4GB of memory while 32bit is limited to 4GB. So if what you had set up before was working might as well just go back to that until you get more RAM.
 
That said... is latency a concern for you at the moment? Like are the guy monitoring the live input through headphones? If not turn up your buffers and that will free up some resources. If they are monitoring you could try increasing your buffers incrementally until it starts to screw up the artists (I find I don't hear delay until I'm getting close to 7-8ms and don't find it bothersome until 12 or more).
 
Also with such a high track count getting recorded all at once you may have a read/write cache issue. Meaning your hard drive can't keep up to all the tracks being recorded at once. In Preferences you can increase these settings (I forget the exact location but it's in there) and it should help. When you are having read/write issues the HDD icon of the Performance module in Sonar will turn red at the moment of dropout and I think it starts turning orange as it's getting strain but that may have been my eyes playing tricks. This can happen even if the CPU and RAM usage are fine.
 
A faster drive(s) can help with that too.

Thank there Beepster,  I have more Ram inbound.  I am going to jump it up to 8 gb, LAtency is no issue as I am using the board for all monitor mixes so that stays in the hardware realm.   As to the read/write cashe  I hope that isn't it...  I am not getting anything lighting up orange or red....

Have you run the DPCLAT latency test? might be background processes interfering. 
I've recorded 14 tracks of audio on a POS laptop with 1/8th  of your specs no problem, but you can't have any red spikes happening no matter what the computer.  

The forum is a wonderful thing. And so is Sonar X3 Producer.

I was starting to think something was up with Sonar because I was starting to get some crackles and pops on my tracking.

I knew there were threads on the topic so checked in here.

Beepster - you are right on in helping me with my crackles. I had recently started straying towards tighter and tighter latencies and not realized I had drifted too far. You're right that I can track/record audio at latencies up to at least 7ms without having an effect on my timing or what I hear to lay down the tracks. I put it at 6ms and I effortlessly achieved clean takes, whereas prior to reading Beepster's reminder I had been thinking there were other causes, like maybe even a Sonar bug. But no, it was my own user error. My song is taking off now, it's awesome. Especially with all the features in X3. I should note that previously I was attempting to record on 2ms latency or even 1ms (I had backed it down to 2 from 1). But at those points I had occasional crackles, so I've now learned my lesson.

Also, the DPCLAT utility looks really good. I would have resorted to that if the Beepster suggestion hadn't worked. The tool looks remarkably helpful. I'm going to store that nugget for the future. Without even using the tool, the explanation page on their website is very informative about finding the root cause of audio streaming issues.