While it is possible to RunLogonScriptSync, I presume there is some reason you don't want to.
You could have the logon script write its PID to the registry at the beginning of the script and remove it as the last step. Your RUN key script could then check the reg in a loop for the PID and compare it with what is enum'd as a loop breaker. This is a belt and suspenders approach since the logon script should remove the reg value but you don't want to let the RUN script goet into a never ending loop.
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