97 subaru legacy stock security problems

Hello,

I'm having a hard time with my security system in my 1997 subaru legacy.  I just installed a new stereo the other day, which i have done before on this car.  (By the way the wiring diagrams on this site for subarus are pretty much all wrong so i posted the actual wire colors on the other form).

Anyway, when i hooked the battery power back up the parking lights and brakes lights flashed as part of the normal alarm procedure.  This has happened to me before but usually i could turn it off by unlocking the doors or starting up the car.

This time however, it did not.  I tried everything i could, used the remote to turn the alarm off, unlock the doors, the trunk, start it up.  Nothing.  Eventually i had to take the fuse out for the security system.   It flashes in a awkward pattern too, it will flash about every second for about 10 seconds then quit for about 5 seconds, then repeat.

I've checked the connections to the security system to see if I messed them up somehow, but they were all in place.

Does anyone else know whats going on?