Dimension 9100 won't start, flashing yellow

I have a Dimension 9100 running XP that won't turn on "normally", there is only a flashing yellow light when the computer is plugged on. After clearing the CMOS, checking cables etc., I tested the voltages on the psu with a multimeter, using a paperclip to short the green and ground, and everything was where it was supposed to be. I eventually was able to start the computer by shorting the green wire with a black one while the connector was plugged into the motherboard, this caused the computer to start up and continue running after I removed the paperclip. I restarted the computer, and it rebooted correctly. But when I shut it down, and tried to start it again with the power button, it didn’t turn on, the flashing yellow light returned. When I pressed the power button to turn it on that time, the fans and drives started for less than a second, then stopped. I also tried starting it with a good psu with no results.

I found other people with the same problem who had said that broken USB ports in the front had caused the problem, so I replaced the front i/o panel with a new one with no results. The ports in front were broken, but the ones in back look okay visually.

Intel Pentium 4 630 Prescott
ATI Radeon X300
650 watt Antec PSU(this original psu was replaced about 18 months ago when the fan inside started making a loud noise)

I don't know what it could be other than the mobo? But if so, how could the computer still start up and run fine like it did?

Thank you!
 
If the broken USB ports shorted out, this could have damaged the motherboard and it will have to be replaced...
 
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