OK
We don't know what model of clock you have. But, It sounds like the Rainbird ESP.
It could be that every time you get to a zone, station, valve on the timer with a bad solenoid it blows your fuse. If you have a master zone, that could have a bad solenoid and cause you to trip the fuse.
That's my guess with out connecting a multi-meter.
The key is finding out which zone is blowing the fuse. This is much easier with the multi-meter.
This is my contribution, good luck.
If this sounds like the issue, you will have to identify the valve in the field and replace the solenoid.

LI0006121, BPAT0011021, CI0009500