Sorry, I didn't realize it was a custom build. Try a BIOS update. Follow
this link and click the blue "download" link. The program will update the firmware for your motherboard. That may get rid of the checksum error.
Why would you need to do this? From the symptoms The OP described, it sounds like the CMOS isn't saving the settings. So unless something in the hardware was changed it is pretty self explanatory as to what to do..
Change the battery.
Re-boot the system, go into the BIOS and reload the default settings, save it and re-boot.
If it fixes the problem then you're done.
If not, do a pin clear of the CMOS and re-set.
You'll get the checksum error after you do this. Go into the BIOS and reload the defaults and save. It should solve the problem.
One thing to be aware of in this process. If you have a different video card in there doing a reset of the CMOS will change the default video to the onboard display. Be sure to change it back to AGP (or wherever your vid card is) as the default.
The absolute last resort (and even Intel recommends this) is to flash the BIOS.
From Intel's support pages:
Update the BIOS on your computer only if the newer BIOS version specifically solves a problem you have. We do not recommend BIOS updates for computers that do not need it.
Unless you need BIOS support that an update will address, messing with the BIOS in this manner is not recommended by the manufacturer.
One would have to assume that the computer worked fine before and the OP didn't say anything about a major hardware change that would warrant additional support of a updated BIOS.