I found the first set of poos totally stained the dipes, but then after several washes it ALL came out. natural fibred dipes usually have a coating on them when new that doesn't wash out for MANY, MANY washes and when this coating comes off, so do the stains.
Make sure you always to a cold pre-wash or pre-soak before your hot soak, and I bet in several washes the poo will come out!
Can't help you on the fishy smell though...
ETA: okay, I didn't realize they were used, my advice was for brand new dipes! I think others here have suggested they may be coated with detergent residue?
Tofie ~ mama to DD1, DD2 and Pookie v3 debuting December 2011
Oh my God....women are the COWS of PEOPLE!! --Reese, Malcolm in the Middle