The ecu will be fueling for the correct boost, if it's leaking boost, then you will be over fueling and could cause problems that aren't evident with no load/boost. It won't hurt to have a good look at all the pipes.
Has this only just started happening?

 

it's a new engine conversion, so i havent had it running correctly yet. I'll check over all the pipes... is there any info anywhere as to where they should all go? as theres still a possibility I've got something in the wrong place while installing it.

 

The early MY93-96 cars have the 3-port BCS and the restrictor pill is supposed to be in the vent-pipe at the bottom:-