I don't have any experience with fenders - but if the problems started after the shop installed the fenders, then I'd take it back to the shop and ask them to fix it. In my experience, in cases when if a shop works on my bike and it's not quite right when I get it back, they always correct the problem without charging me again.
Also - have you called Bike Friday and asked them for advice? (Or were they the shop that installed the fenders for you? I couldn't tell from your post...)
--- Denise