The PWM signal comes from the chip called "Syscon" which is at the middle of the motherbard on the EE side. It has a 4mhz oscilator close to it. It controls the power for the whole motherboard and also monitors the temperature. If the PS2 gets too hot, it will turn it off. Usually the Syscon doesn't speed up the fans if the PS2 is hot. It does speed it up if there's a HDD connected though. I suppose it has to do with more power comsumption from the hard disc so it tries to keep the power supply cool.
Oh ... And if you can't fix the PWM driver by yourself you can aways tie it to a 5V point (refer to romeo mod points for your mobo, or maybe even the Magic 3 5V point ....)
SCPH-10000_GH-001 SCPH-15000_GH-003 SCPH-18000_GH-008 SCPH-30001_GH-005 SCPH-30000_GH-016(V4) SCPH-30001_GH-010(V4)
2xSCPH-10190, 2xSCPH-10350, 2xSCPH-10280
"**** j0 hackers!"
-Sjeep (As seen on TOXIC OS ELF...)