Mike, it has been a while since I last looked at color chemistry, but it sounds like you have a contamination problem. Take a look at:
There is some potentially useful troubleshootiing info in this Fotospeed RA4 pdf document. Yeah, I know its not Agfa, but the chemistry is probably very similar.
The staining may be caused by developer contamination with bleach or bleachfix. It may be a bad batch of developer.
Inadequate washing or a contaminated washing process may also be playing a role. Try re-washing an affected print in a tray.
Brown or black spots or specks can be caused by sludge or scale somewhere in the process. They may also be caused by incorrect preparation of Developer Replenisher.
Sounds like it might be a good idea to clean out the system and replace the chemistry.
Hope this helps