I think there is a mode whereby the immobiliser seems to indicate its disengaged and allows the engine to crank but not start. If you read some of the older MGF forum posts it seems to be a common problem after a car is laid up over the winter. Indeed, i had this problem myself. I never did find the root cause despite having access to a PSCAN unit. I spent days trying everything, charging up battery, changing fob batteries, did an unlocking of the car using the EKA, checking fuel pressure, spark etc then one day i got in and it just started and has been fine ever since. Another person had the same problem and had to change the MEMS ecu, immobiliser ecu and key fob as a matched set from eBay to get his car to start. He donated the bad set to PSCAN to see if he could find out what the fault mode was but i have not seen any posts on the PSCAN forum to indicate an update on this. I can only suggest you keep trying to lock and unlock the car using the fob, key and maybe EKA code if you know it. Do this half a dozen times with a decent pause between locking / unlocking before trying to start the car. Good luck.
Nigel