Originally Posted by CaptainCPS-X
There is an option on the Game column on the PS3 XMB "Memory Card Utility [PS1 / PS2] where you can create "Virtual Memory Cards" then assign them to the desired Slot. Then when you load a game the memory card will be already mounted , it doesn't matter if you loaded with Breaker Pro, multiMAN, or even Cobra Manager.
I did try that before trying to find out why the savegames do not work and it didnt fix the issue.
Booting a PSOne game resets the memory card being unassigned to any Slot.
Are you sure it works?