WD3200AAJS 320GB HD not recognized until accessed from DOS

The only thing I can think of is that the PM2 jumper may be in the wrong position. WD’s documentation is confusing – some models use the jumper to disable PUIS, others use it to enable PUIS.

According to the ATA standard, the jumper takes precedence over the Set Features command:

“When enabled by a jumper, this feature set shall not be disabled via the SET FEATURES command.”