I've had this very problem! Here's what happened...
1. got an I-opener (still haven't figured out what version (v1 or v2) i have)
2. Got a bios chip and HDD kit from BadFlash
3. Installed everything...
I then came to notice that my IO wasn't saving my bios settings. I took the battery out and tested it with a multimeter. I was barely getting half a volt from it so I figured this unit was sitting around for a good while and the battery up an died.
I pulled a cmos battery from a dead motherboard I had lying around. It rated around 2.5volts so I put that in the IO. No luck! While putting the battery in I wound up breaking the two positive prongs on the battery holder. The prongs touch the top (+) of the battery to make the connection. So, then I figured that the battery simply wasn't making a connection and therefore was not saving the bios settings.
Went back to the dead motherboard...(Never throw anything away!) and broke off a prong from the cmos holder. Came back to the IO and soldered it on where the original prongs broke off. Tested it with a multimeter and i was getting 2.5v across the - and + of the cmos battery holder. Electrically, this solution should allow the bios to save the settings I want it to save.
NO LUCK! Used my multimeter to find shorts, but didn't find any! Stumbled across the forum trying to find an answer, and I found one. (sort of, thanks to no energy)
Using Badflash's HDD kit, the hdd does sit awfully close to the cmos battery. I didn't find shorts, the battery holder was electrically in order....so I decided to put a piece of folded paper between the hdd and the cmos battery...(grasping for straws here)...put the IO back together and powered it up. Set the bios settings the way i wanted them and booted windows then shut down. Pulled the power cable from the IO and left it alone for about 5 min.
IT WORKED. The IO saves the bios settings I made now. Hope this helps someone!