Chris,
There is no problem with your drive.
It sounds like you are running the operating system and PC-Doctor from the Seagate drive when the test times out. Disk accesses while a SMART Self-test is running can affect the time a test takes to complete; This is likely the reason you are seeing different behavior when running the Seagate as the master or slave drive.
The version of the product you are using is improperly returning a FAIL result under a timeout condition. This issue has been fixed in newer builds (Your build is based on code from Sept 2005). Timeouts are not failures, it just means that our diagnostic thinks the test is taking too long and will never complete - so it attempts to cancel the test.
We have run into problems (especially on larger drives) where applications accessing the disk prevent SMART Self-Tests from ever completing. Disk access cause the drive to preempt the self-test, and then after servicing the command they resume the test. Most drives handle the preemption well, but some drives do not and will never finish a SMART Self-test depending on drive activity.
The build you have installed predicts a timeout on a SMART Short Self-Test if the recommended polling time (reported by the drive) exceeds a factor of 2.5. Your drive has a polling time of 1 minute. The first test completes in 1 minute, 6 seconds so no timeout. The second time you run the test with the Seagate attached to the master controller, the test decides to quit after the test has not completed after 2 minutes, 36 seconds (exceeding the 2.5 factor).
The value of 2.5 was found to be a bad timeout on some drives and newer builds use the value of 6.0. A timeout can still occur but is much less likely to occur.
If you go into the PC-Doctor 5 installation directory, you can modify the timeout factor by opening pcdrsmart.p5i and finding:
Test.SMARTShortSelfTest.TimeOutFactor.value = 2.5
and changing the value from 2.5 to 6.0.
About the Extended Self-Test :
The test is likely still running but is running much slower than normal. Normally the extended test on a drive that size will take a little over 2.5 hours. Does the Seagate disk tool take longer in the master configuration and does it finish the test?