Here's an official document issued by Trek on its history: http://www.vintage-trek.com/TREK_History1.pdf

It points to quality control issues in the mid 80's, and especially a problem they had with the 2000 model, a bonded aluminum frame. There were actually a few well made bonded aluminum frames (Raleigh Technium among them), but I think Trek's failure must have spelled the death of that particular method of framebuilding.

Some don't like the flexy ride of the larger-framed Reynolds 531 Treks, others love the cushy ride. I've heard more than once that some of their early models had weak seatstay to seattube bonds that failed prematurely. I have personal experience with a frame that has one seatstay longer than the other (simple fix is a slight wheel redish) and a VERY low rear brake bridge. So, quality control could have been a bit better. Frame rides great, though.

These kinds of problems can be expected with any frame, however, especially mass produced frames like Trek.