Flashing immobiliser light once engine running

[KitsonRis]

Tried to search for this but couldn’t find anything.
Went to start the 172 yesterday after about two weeks not moving it. Battery was flat, but then for some reason I left the key in the cranking position for a few seconds after it had died, wasn’t cranking over, then it kicked into life. Then the immobiliser light was flashing like crazy while the engine is running. Engine was also running rough, but I thought flashing EML was injectors? Went to pull away and it stalled because it was firing on any number between 1-4 cylinders. Started up again fine and no flashing lights (but still ran crap).

Ive not seen the flashing immobiliser light once the engine is running, did it just get confused when battery was drained then kicked back into life? Want to rule out stuff for why it’s running rough (although think that is because it’s got damp in the recent rain and not been used) so I can get it sorted.

 

[KitsonRis]

Will also add that this morning it didn't do all this flashing stuff once running, but the key wouldn't work the central locking and then the alarm/hazzards were on, then stopped, then started again. Was also very lazy to start first time. Then after about 20mins of idle I turned it off then back on and fired up first time with no problem. Wondering if it is because the battery was flat and it didn't have enough power to disarm the immobiliser properly and just got out of sequence. Will monitor how well it holds its charge.