Right.
That's because on T904 (the standby transformer), the auxiliary winding gets its power from the main winding. Basically IC907 (standby PWM controller) "tells" Q908 (the standby MOSFET) to pulse on and off very fast. The pulses (ac voltage) of Q908 are sent through the main winding of T904, which results in an output voltage at the secondary side of T904 and the auxiliary winding.
But we already have disabled the primary side of the standby circuit, remember? (the removal of J5 and R974 disables Q908 and IC907). Therefore, you don't need T904 connected at all for this mod, just two external power supplies - one is the 12v computer PSU feeding the standby output, and the other is the ungrounded power supply feeding the positive side of electrolytic capacitor C958 (this makes it seem as if the voltage is supplied from the auxiliary winding of T904).
Well, I looked through the TEA1507 (IC904) datasheet again, and it says that the minimum start-up voltage is 10.3v. Therefore, use the 12v, 1500mA linear power supply. I don't think a regulator IC will be needed.
No worries. I do that too sometimes

I think this is why I didn't see the potential problem that was caused by the missing auxiliary winding voltage.
By the way, those capacitors you used for the replacement are huge! What brand and series are they?
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