That's the first time I'm ever heard of a problem like that! You have to remember that during loud peaks in a Dolby Digital/DTS soundtrack, the subwoofer (in a THX 80 Hz crossover set up) may have to reproduce up to 120 dB, which is very loud and demanding.
I'd suggest introducing a low-bass roll-off, like the one used in the THX boundary gain compensation filter. I have a THX Altec Lansing system, and I find that this works reasonably well. In an attempt to clean up the bass response, I did once try blocking up the ports on the subwoofer. It wasn't very effective so I leave the ports unblocked.
I don't have a THX sound card so I don't have the THX boundary gain compensation option. I use a simple equaliser on my sound card to introduce a more severe roll-off than the THX filter, -3 dB at 125 Hz, -6 dB at 63 Hz, and -8 dB at 31 Hz. I don't watch many films on my computer, but I'm pleased with the results when listening to music.
Another thing you could do is to lower the low frequency effects channel volume.