I'm having some computer issues lately. I use Amplitube and guitar straight to my computer through line-in.

When I play, everything will sound okay, and then it will stop. This doesn't just occur with Amplitube, but any VST effect I've tried. In Amplitube, everything will start off fine, and then I'll play, and it will be like there is nothing happening- no meters, no sound, nothing. But if I play just the dry signal from line-in, I will have no problems, but the sound is awful quality. Also if I bypass the Pre model in Amplitube, it will last a little longer, but the problem still occurs. I've also tried using Voxengo Amp Simulator, the same problem happens, but it will last a little longer, but still the problem occurs.

The same thing happens if I use the RSE in Guitar Pro. It will start off okay, maybe play a few bars, and then it will not work. The score will play, but no sound. If I use MIDI with Guitar Pro though, it will work fine.

I'm totally lost as to how to fix this problem. I have two soundcards that I use- A Soundblaster Audigy SE, and a SoundMAX which is on my motherboard. I have to do things this way because the Audigy can't record with ASIO, and the SoundMAX's green output plug is broken.

I've tried updating drivers, uninstalling and reinstalling programs, and nothing works.

Sorry for the long post, but I tried to be as detailed as I could in describing the problem, and I'm just frustrated with it. So any ideas would be much appreciated.
How about trying a proper audio interface such as an EMU 0202 USB or PreSonus Inspire?

I never had great luck or quality with stock sound cards. They simply are not made for recording and so you wont get that quality sound or 0 latency monitoring.

When was the last time you reformatted the PC and started off clean? Sometimes PCs will start to slow down and act strange, even more so if they are running slow from general use over the years. I try to reformat my desktops and laptops at least once a year and it really helps quite a bit.