Appreciate the reply, but I figured it out.
If quark is launched before Suitcase, the XT plugin will uncheck itself.
They are clicking the Quark launch icon the second the machine boots up and some have Quark auto-launching. If quark is launched before Suitcase, the XT plugin will uncheck itself. This explains the random cases I get from my users. Pretty much a crapshoot if Quark loads before Suitcase and visa versa.