I wonder if one of the fuses, though of the proper rating, is a defective fuse or perhaps installed in such a way that something is shorting across the terminals.

Though, if that is the case, it just means that you'll be blowing fuses all the time instead of headlights. Albeit cheaper, though equally annoying.

Do you have access to a shop manual or wiring diagram of the car?
I wonder if there is some sort of transformer or voltage converter feeding the headlight circuit -- though I'm fairly certain sealed beam Halogens run off straight 12V DC.

Another thought is that a flaky alternator could be injecting noise spikes into the system that wouldn't trigger a slow blow fuse.

Have you checked the Empeg FAQ entry about tracking down grounding problems?

Maybe an iffy contact in the headlight switch or somewhere in the wiring harness could be causing the lights to jiggle on-and-off rapidly enough that the light remains fairly constant but you get a lot of on/off transients through the filament while driving.

If all else fails, maybe you could install tonyc's old breaker panel in series with your fusebox....