Perhaps the injector opening time was too large.

MS1 with the extra code is not the optimum solution for running large injector in relation with a small engine, but 480cc injectors with a 2.1 engine shouldn't be that bad really.

What req_fuel did you run anyhow? Previously and now. The standard setting, if you are starting to tune from scratch, is 15. This would result in exactly what you desribed if you didn't correct it and just started to tune the VE map right away.