Them Pioneer 6300's have a wide array of controls for the pre-outs. I am thinking they disconnected the battery resetting the radio's settings. That's the only thing I can think of that could have happened when putting in an alarm.
How knowledgeable are you with the use of all the functions on the deck??
Sorry I wasn't more help... real difficult to tell you what the problem is without hearing the problem.
Thomas Kenyon
Custom Sounds
San Antonio, Texas
210-340-4000