Does the money get deducted at the end of month?
If not, it's possible the game's CoreScript partly or completely stopped running, although a sufficiently severe failure here would break multiple things (star systems not being marked as explored on entry, monthly financial report not appearing, among others), and I don't know what mod would do this.
Quick Console Commands runcode to check (copy and paste):
runcode for (EveryFrameScript script : Global.getSector().getScripts()) {
if (script instanceof com.fs.starfarer.api.impl.campaign.CoreScript) {
Console.showMessage("Running core script " + script);
}
}