Have no transmuter to test this on, but I'm pretty much certain that it cannot be UI related. The reaction counters are automatically populated by the game, it's not the UI doing that. You can try renaming your uisettings.ini and start with a fresh UI setup at least for testing - maybe something is corrupt in that file and messing with your counters. Unlikely but I suppose not impossible. Otherwise you can delete eq2ui_tradeskills.xml from your ProfitUI folder to use the default UI file if you prefer.
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