It may just be your washer, I had a terrible time with my fl and finally got rid of it (only 2yrs old

) and got a top loader and have never stripped my diapers in just over 18 months ago.
That said I would do hot washes with no soap and check for suds. When you wash normally do you do hot rinses at the end and check for suds? I think that really helps. That is what I do (I use charlies as well) I have found with charlies it will take 1 to 3 hot washes with no soap to get to no suds but with other detergents it is 5 to 7.
Other methods of stripping you can use a T of dish soap (some swear by blue dawn) and then rinse rinse rinse on hot till no suds. This will take forever so I would only do it if just good rinsing doesn't work.
Do they smell out of the washer or when peed in? Smelling out of the washer usually means they arent getting clean enough. Smelling when peed in means they have detergent build up. (usually not always)
Good luck! Any more questions ask away! Welcome to MDC!