I think it is because of the portable Flash plugin Chrome Portable uses (and Firefox Portable doesn't). It's called PepperFlash and has it's own private Flash-Cookie repository, while Firefox Portable uses the system-wide shared one.
It only saves the gold credit, but not the upgrades. :(
The bug exists for me and several others as I can tell from their comments. But apparently not for everyone, as their comments got downvoted.
 "Amberial Axis"){kind=icon}
 "Burrito Bison"){kind=icon}
 "Heavy Weapons"){kind=icon}