Freelander 1.8- has it been chipped??

I've had a Freelander 1.8 for a few years now, and it has a very odd engine problem which I think is long standing. The long term fuel trim is at -20 to -25%. Also it soots up the exhaust tail pipe under certain conditions- it seems to happen at full throttle at low revs when the engine management goes open loop. (it's MEMS3, 2005 model). There is also a rare starting problem which I think may be connected- every few months it refuses to start until the engine is cranked for half a minute or so- then it fires up on 1 or 2 cylinders, then 3 and then 4. As if it was flooded.

I've checked or substituted: fuel pump, injectors, MAP sensor, throttle position sensor, CAT and lambda sensor. Intake and water temperature read correctly. Emissions are fine according to MOT man, and you can see the lambda sensor switching fine in closed loop mode. Management light is off.

Could anyone suggest what might be wrong? It's almost as if it's expecting different injectors to the ones fitted. (which are MJY100550, light blue). I'm beginning to think someone's chipped it in some way. I have done some minor breathing mods to intake and exhaust but I would expect that to increase fuel demand over what's expected. It's actually running really well- I'm just concerned that soot could damage lambda sensor or CAT.