I picked up a programmer that has logic testing and all the 74 series chips passed multiple runs.
Doesn't mean there isn't an issue but they test ok. I had already replaced those particular chips anyway.
What video card are you using on yours? Mine is fine with an EGA/CGA/MDA, but all three VGA cards cause the problem but only during VGA/EGA bios initilization.
It also has no issues booting just from floppy, with the XT-IDE card uninstalled.
It's also always 400 Hz tones, despite what other sounds might have been played at the time. For example, during Champions of Krynn, the beep has occasionally happened during music/gameplay sounds, and is still at 400 Hz, which make me think that there's an explicit bit of code somewhere that's setting the sound timer to that frequency.
All pc speaker sounds would tinker with timer 2, right?
Sergey's bios appears to specify a 400hz tone for two reasons: CPU failure and low memory error, in bios.asm. Both of those appear to only fire during power on self-testing, and neither should be setting a timer to 400hz unless there's a "failure" condition?
Since the XT-IDE card causes this problem pretty regularly, I might go in to the source and start spamming debug output to the post card that's built into the malinov backplane and see if anything pops up...