Mariner Fan,

Sounds like classic "ghost shifting" to me too. Like Moo said, this happens when you stomp on the pedals sometimes. The BB deflects to the side and this stretches the cable. It can be severe enough to cause the friction shifter to move a bit and thus, when the pedal stroke goes round the slack in the deraileur cable will allow it to shift down to the next smallest cog.

Often, tightening the shifters a bit will be the cure. Also, be sure to lube the cable well where it passes through the BB. Your bike has unique cable routings and you may need to appeal to the Trek gurus to get the kinks worked out. I've heard of problems both at the BB and at the point where the RD cable comes out of the chain stay. The chainstay problem can inhibit good indexed shifting. And (on all bikes) binding of the cable near the BB shell can contribute to ghost shifting in friction mode. Several folks on the iBob mailing list have this type of bike so it might be good to ask there too.

Lastly, if you are 200lbs or more or if you are a really powerful rider, the BB sway you are getting may be due to you hitting the limit of frame. Newer oversized steel tubes do a better job of stopping BB sway. Although, if I recall, that frame is 501, not 531 and I would expect the 501 to be noticably stiffer.

I would look at the BB cable routing first.