... Sadly I don't have access to a proper oscilloscope - I used Xoscillo on an Arduino to build it. ...
I don't know anything about the open-source Xoscillo code for Arduino (yet), but it appears this would be adequate for troubleshooting. Perhaps you can look at the code and create a loop that samples several things, like the op-amp output and the PWM output, over a period of whatever depth the sampling memory affords at a suitable sampling rate. Then, when a "trigger event" occurs, the loop is interrupted and the contents of the stored samples are displayed. Perhaps a few hundred samples after the trigger event could also be captured to see if anything else is going on. The trick will be to figure out how to determine that the PWM fan controller has "locked up". Perhaps no output pulses with the analog input in a valid range would be definitive.
