Alarm sounds when locking car

[Blazingblacksmith]

So just had a new abs pump fitted on my 2010 Outback diesel estate. It was a Legacy pump but all numbers etc matched so should be fine. When my wife got home from the garage and tried to lock the car with the remote it beeps loudly for about 30 seconds and then the alarm goes. Cant believe its anything to do with the abs pump but any ideas on what it could be. Also just noticed that it is not recognising going into 6th gear on the dash and just says its in 5th. 

Locking the car using the key works but then the alarm is not armed.

Any ideas would be very welcome. Tried disabling the alarm by holding the unlock button on the drivers door and opening the door but that does nothing.