The second thought is that maybe the PSU itself isn't capable of providing enought power for all of the components. And: warmed-up components may draw more power.
FWIW I had the same problem when updating my Mystic to the flashed version of a 9800 pro card (taped pins). The general consensus found by browsing internet forums was that there just wasn't enough power in the OEM PSU (360 watt?) to handle everything (2 internal SATA, 2 ATA drives, DVD drive, and 9800 card). This thought was reinforced by the fact that only one of the SATA drives would boot up, but work fine with the other disconnected, or with the original card re-installed.
As fate would have it my 10 year old OEM PSU failed shortly after installing the card,,, perhaps it was on it's way out anyway? Problem solved by replacing it with a 500 watt PC PSU, though I have had some intermittent sleep issues (crashes), presumably from the PC PSU not having a 28 volt standby voltage lead into the motherboard, which again presumably could be corrected by adding one independently or other hacks, which I haven't felt compelled to tackle.
Replacing the PSU with a PC version is not for the faint of heart as it involves rewiring 22 output leads to the corresponding correct voltage inputs on the motherboard, and possible mounting issues, and may not be feasible with other G4 models.
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