As I recall, the PicassoII is supposed to Autoconfig as 2 devices, so you're okay there.
Are you running 3.9? Back when I used a PicassoII, it had some issues with the ROM Update - the board would autoconfig from a cold start (meaning, checking Early Startup Control right after powering on), would not be detected afting kicking in the 3.9 Update file, but would be detected on subsequent warm reboots (triggered by Ctrl Amiga Amiga - reboots triggered by software wouldn't work).
Give it a warm boot a few more times and see what happens.