Ok so got a problem with my wife's 2010 Avenger SE 2.4l, I replaced the alternator a month or so ago and ever since then the anti theft and key fobs have given us nothing but trouble. Hit the unlock button in the morning and the headlights flash but nothing unlocks and alarm does not disengage. Open the door with the key and the Alarm goes off until you hit unlock with the fob and it will finally turn off.

At first figured ok inconvenient but we'll get to it eventually however recently it's started affecting how the car runs as well. Sometimes it starts fine, sometimes it's really rough and will not stay running. The times that it does start fine it'll run ok then die suddenly at random. Could be 10 minutes, could be two hours. The reason I feel it may be related is I've noticed that when it does happen the anti theft light on the dash (red circle) will occasionally flash as you're trying to restart it.

Read on another forum that hitting lock and unlock with ignition on (car not running) may reset everything, and it does for about 10 minutes then it's back to the same issue. Tried turning key to on and leaving it in ignition for 60 seconds then removing and same thing, works for about 10 minutes then same issue returns. I've checked battery voltage and it's good, and the alternator is fine so at this point I'm at a loss, any advice welcome.

 

The Run Relay is inside a small black box, the closest of four relays to the driver's side front fender and just to the rear of the fuse box or TIPM
Trade this relay for any of the others (Which are cooling fan relays), as they all four interchange.
IF this doesn't work trade for the next one.
IF this doesn't work try anything I tried in my dilemma post; 2009 Avenger FOB failure and more.