Just for testing, have you tried flipping the condition (of the flag is on, instead of it being off)? It's been a while since I edited any of my conditional macros, but I'm pretty sure there is an "else" option. You could try using the "flag is set" for the primary condition (and either put in a dummy module to activate, or I think just a delay would be enough), and then the "flag is set" could be the "else" condition. It should only take a few minutes to test that case.
Alternatively, if the universal module and the macro are always being triggered at the same time, why not put the universal module's trigger into the macro? Use the "else" option, so it gets triggered either way, and only have the flag affect the other module.
But even if it is a bug, there isn't going to be any further development of AHP, as the source code was lost in the transfer of the assets to Authinx. So the only options you have at this point would be to try and work around the problem, unfortunately.