I have and use a CP31 (also have a CP51) but with Kodak RA-RT chems. Have you eliminated the following variables:
time and temp on the CP-31 (e.g. what temp, and for how long in the baths? I use 34C and 280 (mm/min?) setting on the CP-31)
Order of the baths - prewet? stop? ( I do Dev, Blix, pre-wash (then Wash in CP-31 WD unit) as my bath order)
fogged test strips? Maybe tray develop one and see what happens...
IME, Kodak RA-RT, even in mixed form, is pretty long lasting. Unmixed it's even longer lasting. Not sure on the Fuji chemistry - but I'd think it should be stable for at least a year unmixed.