sounds good,

If the HT PSU ignites the tube on test then that is ruled out as that bypasses everything in the safety system.
Leaves the Low voltage rail supply and the main controller card

Do you have the means to test the outputs from the low voltage supply? (ie: stick power into it and probe the outputs)

If it's not the LV supply that will likely mean the controller card. They can be easily damaged by a short of voltage spike (and ironically a spark out is usually heard as a tick or low volume crack as one of the tracks pops)