Chances are it's a matter of not having the right load on the flasher unit, assuming you still have the old thermal unit in there.
I replaced mine with a standard DOT-552 electronic unit, and no more flashing issues.
With the correct load it should flash down to like 11.5~ volts, regardless of whether the engine is running. If you have the wrong load in one end, it may flash too slowly or only above 13~ volts. Goofy stuff.