I had a similar problem that when I would use my emergency flashers, they would work just fine, then the regualar turn signals would go out for a while then come back on magically. quite a pain, but it turned out to be the multi-disfunction swich. I had a friend and expert take it apart and clean it and it works like new now.
as for your problem since you are sure you have a good switch, my next instinct would be either the flasher as another has mentioned, or the power wire that supplies power to the turn signals, which will be different from the flashers since the flashers run off a hot at all times wire, and the turn signals are off a hot in run wire. I can't think of any other function that would run off a hot in run power source, that would be a good way to test the theory easy. but I would check that. someone with a service manual, can you post up a diagram of the pins on the multifunction switch of this year? find which pin is the hot in run wire and test it with a voltmeter, see if you get good power. another thing I just thought of though, is the flasher in the turn signal circuit before or after the multifunction switch? if its before the switch, then you should see a flashing 12V signal on that turn signal input power wire when you have either singal on, if you get that, and the switch is good, then you know your problem is in the wiring afterwards. probably not the case, if you don't get a good signal, then I'd check the flasher. if the flashers turn out to be after the switch, then you should get the constant 12V in run signal as I described above. hang on for a little while and see if anyone has a shop manual and can post a wiring diagram, if not, I have one for my 97, but I know the multifunction switch is the same...maybe the wiring is too? but best to get a gen 2's diagram is possible.