Hit P (preferences)
Click File on the Left
Click Audio Data Sub category
Set Record Bit Depth to 24. There's no reason to record at a bit depth that exceeds your device.
 
This should help.
 
Also, since you are using RME, you should be aware of DigiCheck (see their downloads page). There are new drivers and version of DigiCheck out for Windows 8.1 btw.
 
You can record all your devices channels to a single file using DigiCheck which saves you a huge amount of overhead. Sonar writes all the tracks to separate files (and reasonably so). If you switch to write the tracks all to one file when making a recording you can dump WAY more data onto the same hard drive. When I'm just recording a gig or a continuous performance, I always use DigiCheck then mix in Sonar.
 
Sonar is great if you need to play back anything that the musicians will monitor as the perform, like soft synths, metronome, or guitar synths. That sort of thing.
 
For me, with my UCX, the interface has EQ, compressors for every channel as well as reverb and delay on busses. It's a complete solution for mixing live.

toledoo1
...  I also noticed that this happens mostly when playing notes for the first time, but when i play a melody several times the pops disappear, but when I introduce new notes to that melody then it comes back...

Ah, yes.  You really got to warm X3 up first.  You got get those revs high before X3's turbo kicks in.

You might try the following settings, just to start with something that does not push things to perhaps beyond their capacity:
 
Sample Rate 48k
ASIO Buffer Size 128
Record Bit-Depth 24
 
The above are just a starting point.  If the above settings get rid of the cracks and pops, you can start upping the sample rate.
 
One nice thing about the above settings is that they produce a pretty low latency - my input and output latency reported values are 3.9 milliseconds each, and I have a total round trip latency of 7.8 milliseconds.  Your reported values were about 3 times higher than mine.
 
So, how about trying the above and posting back?
 
Bob Bone
 

Hello again everyone and thank you all for helping.
After much of trial and error, the problems seem to be indeed related to the second sound card's driver (Creative) and external HHDs speed. But still X2 seems to handle this situation better than X3. However, I am not going back to X2 after trying X3, no way. I will try to get new faster HHDs and hope for the best.
 
Thank you again.

Did you try turning your sound card output down just a little. That happened to me when I upgraded in 2010 to Producer 8.5.3. (which I am still on, but thinking of upgrading soon).

What VIs are you running? Once I switched many of mine over to SATA III SSD's, all of my pops and clicks disappeared. Also, if you are running "energy efficient" HDD's (or 5400rpm drives), that's also an issue.

I am probly way off base here, but when I first fired up X3 and played around. I noticed all of my plugins were rearrainged. I grabbed guitar rig and was plunking away and noticed cracks and pops. after further checking I realized I had the 32 bit version loaded while I was in the 64 bit X3. I swapped it back to Guitar Rig 64 and whalah...no more pops and cracks. I'm sure you have checked this, but just in case....:)

Don't know if this applies in your case, but I solved a lot of "pop" problems by buying a separate USB card for my motherboard and plugging my interfaces into that card. The hard drives were putting "dirt" on the motherboard's USB ports.

Thanks for all your suggestions, appreciated.
The problem was solved after several tries by doing two things:
1- re-install the sound card drivers.
2- delete the AUD.INI file from the X3 folder.
It seems that X3 was using the AUD.INI file from the X2 folder (or copied it from there).
Everything is working perfectly now, only limitations I am encountering now are due to external hard drives which I can live with for the time being until I upgrade them.
So, thank you all again for your help, and especially dan le for suggesting this method.
 
Have a good day

I was having similar problems with X3 Producer at first.  I changed my vst scanning from background to startup and then rebooted my computer.  It has seemed to work fine since.  I hadn't changed any other settings since switching from X2 Producer and I never had any problems with X2.