Okay, this just started happening, don't ask me why. I use a Quad Capture as my main audio engine. I plug the POD HD SPDIF out into the quad as well as the regular analog stereo out. This way I can monitor my recordings with amp sims provided by the pod but only record the dry signal from the SPDIF. I have been doing it this way for years. Suddenly the audio starts cutting in and out at regular intervals in X3. All audio disappears, not just the POD. If I shut the pod down. Everything plays fine. I don't have this issue with any other software except X3. My sample rates are all synced, I haven't changed any settings, intentionally at least, and this is an on again off again problem. I use the quad for all audio duties I don't use the pod's built in drivers at all. What the heck is going on here? Thanks in advance for any help.

O.K. then...Looks like a Cakewalk tech support call is in order here...

It actually might be the quad capture going out of sinc via spdif.
I presume the clock in your asio driver is set to ext spdif. These can sometime go out of sinc with each other; the analogue still works by the sounds of it.
 
This has happend to me on now and then using a Motu2408mkIII.
I just switch of everything and reboot.
 
A sonar thing that used to happen many versions ago was no audio in or out.
Solution was change the preference from asio to some other source like wdm, reboot both computer and interface. The once the wave profiler does its thing, change it back to asio and reboot both. This was an old Sonar issue I ran into back in version 6 or 7.
 
With the HD PRO you also have a DI out that can be for a DRY input to your interface.
 
I personally prefer the onboard amps from my HD500 than using a simulator.
Amp sims sound very thin to me on the treble strings and  two dimensionally lacking depth.
Here is the trick to test.
with your amp sim crank the gain and roll off the guitar volume play on the E and B strings. Even without rolling the volume off on the guitar amp sims get thin to my ears.
Do the same to the HD PRO amps.
Maybe amp sims have gotten better over the last year or so.
 
I do understand that in the mix you want cleaner and dryer with FX than what sounds great to track with.