Alarm messing up OBD-II scanner?

Check engine light has been on for about 300 miles until it went off today. Went to Autozone to have them pull the code(s). Guy hooked up
the unit and it made the alarm chirp and the door locks open/close but that was it. Truck is '95 Ranger 4.0. I bought it used as-is; think the alarm is after-market eventhough the transmitter says Ford on it. Am going to figure out how to turn alarm off or put in vallet mode and try again, but does anyone have any suggestions on what i should do to fix this problem? Thx.
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