I have a short inseam as well and have had problems with waders leaking where the inside seams sag and rub. In my case, it's not so much the crotch as the inner thigh and knee.
I spent a few extra $s and got some Orvis waders (http://www.orvis.com/store/product.aspx?pf_id=2G52) for my most recent pair. These come in a short inseam size and they also have a design the eliminates the inside seam. So far so good with these, but I've only used them about 40 days so far.