well maybe it had nothing to do with the battery going flat, as since ive had it, the battery has been completely disconected and it was fine, so maybe they are 2 completely seperate problems.
I very much doubt the current settings have anything to do with the last tune as most of them are set to the max they can be, (ie rev limiter is over 31000, and most of the others are at 99).
I just got an email from matt who i bought the car off and he said he has the settings which the previous owner wrote down after the tune was done. so ill get them off him, put them in and see how she goes. and If it does it again, then... i dont know... maybe its time for a better ECU.