See if these sound differently, if you can.

http://www.parodius.com/~memblers/sweep1.nes
http://www.parodius.com/~memblers/sweep17.nes
(can't use the URL tag twice, for some reason?)

In these roms, I tried disabling the sample playback (with $4015) before the delay loop begins, and reenabling it afterwards. Would that help? sweep17 tries a 17-byte sample (all 00) just doing the same thing.