The way the light flashes, is actually an error code. You can look up the codes on the Apple site, or look in the Mac pro's manual in the trouble shooting section.
The most common flashing code is for memory errors, usually when no RAM is detected as installed. Have you been inside the Mac Pro, maybe bumped the RAM?
Anyway, check what the codes mean.
Also, try removing your new UPS to see if that makes any difference.
Tom N.