You can see that I have a RETURN statement at the end of the routine that is called to service the interrupte, so I presumed the @INT_RETURN that is the next statement after the RETURN would take care of flags.
It would if you had called the routine with a GOSUB instead of with a GOTO as you currently are doing:
Code:
'-------------------[ Begin Interrupt Handler }-----------------------
AlarmHdlr:
    Goto Alarm     ' Call Alarm handler subroutine in INCLUDE file
@ INT_RETURN