Strange phenomena after upgrades

Dear People,
I recently went through a number of changes to my Mac G4, dual 1 ghz in anticipation of upgrading an ImagePrint RIP & improving the performance of PhotoShop - specifically opening large files (248mg), saving, saving as, copying, etc. The other night after shutting everything down I returned to the studio which still had the lights off, and the monitor light was pulsing off and on. I went over to the CPU and pressed the power button and it would not start up. I waited and eventually the light ceased pulsing. The CPU then fired up. The monitor is the original 22-23" Apple cinema display which is plugged into the CPU. I closed the door and hoped this was one of those self-curing computer quirks. The next night I watched and the same thing happened. The light pulses in a loose cycle with intervals between, and eventually stops after about 30-45 minutes. Should I leave the computer on all the time (hard drive & monitor asleep), or does the flashing light foretell of some future disaster?

Changes I had made & at the moment it is running very well:

- changed original scsi hard drive to 15,000k MAU series Fujitsu HD
- installed latest firmware to ATTO UL3D video card
- fresh, latest copy of OSX3.9.9 (I had asked John at ColorByte several months ago if 3.9.9 would run ImagePrint and it does!)
- installed Sonnet firewire card - ports on CPU had become "flaky" and the card solved the problem
- installed ImagePrint 7 to drive Epson 7880
- PhotoShopCS
- Silverfast Ai to run Nikon 9000 scanner (which should put speed into percpective)

Sincerely, Michael