Okay, fixed it myself.

I added a PAUSE 10 as shown.

But I surely do not know why the fix worked!

Code:
         . . .
        READ 254,PFLAG                   ' Get state of memory protection
        IF PFLAG=1 THEN GOTO NXTEST      ' If "on", skip mode select

        PAUSE 10
                                         '      CHECK FOR "STRAPPED" INPUT
        FOR INDEXW=1 TO 500              ' Test for TRIGGER status at startup
            CTLIGHT=1 : ALIGHT2=1        ' Indicators are HIGH during the test
         . . .