thanks, it's working now thanks to Kingcreeper, but I'm sure that advice will come in useful at some stage
One thing to keep in mind, when you do a flip (not sure how you did it, but I am guessing with the scale tool and just changing the x axis to -1) you can sometimes end up reversing the normals... so its best to recalculate the normals when you do that otherwise you can look through it right into the inside of your mesh.