If you don't have a GPIB analyzer, try attaching a scope/dmm to the SRQ line to see what value the line has during that timeout period. (The SRQ line is pin 10 and ground is Pin 24.) <0.8V is asserted. If the line is asserted, then something is wrong with the GPIB card/driver. If it is unasserted something is wrong with your instrument or cables (ie SRQ line is not connected). Please post captures with VISA unchecked, so only the NI-488.2 calls are captured.
As a side note, your last spy capture does show the wait on event waiting 60 sec, however, I can't find the driver call where you set that value. When I look at the previous SetAttribute calls, all I find is a timeout of 5 seconds being set on line 3. Do you have
any idea why?