If a simple reboot corrects the problem temporarily, I would suggest that it is not a heat related issue.
You stated that you have removed and reinstalled the drivers and the card. A reboot would not correct a hardware problem, but a driver problem or a memory leakage issue might be temporarily corrected.
Distortion might be a capacitor issue as well, although generally a capacitor failure will not be intermittent, but sudden, and I cannot imagine a reboot correcting a capacitor failure (other than discharging other caps around it).
I think your best bet is to start simple first. The next time your sound gets distorted, try unplugging your speakers and either using a headset or just reconnecting them w/o the reboot. It's possible you have some oxidation on your connector that acts as a small resistor, thus changing the voltage drop at, and current to your speakers. I doubt that though.
How much time are you talking about when you say it takes some time for the distortion to appear? Is the time almost exact each time? If so, a bad capacitor is very likely.