I have heard that HCA sometimes might bleach the print. I use permawash and have not seen any of this. But there is definitly a problem if you are seeing a change from the developer to the clearing baths. If anything the print should look better. Why dont you try EDTA or HCL baths and see if there is a difference?
I suppose this is the holy grail of every pt/pd printer, to find a paper which gives the same image wet and dry. But my recent expereince has shown me that sometimes the dry down helps "set" the image and it looks even more awsome.....I guess I got lucky with this last batch of negatives.