Thanks.
Yes I've managed to do it in two passes. First writing both ID3v1 and ID3v2, then remove the ID3v2 tag. At least I think I have - I've thought myself into a state of confusion over this so I'm going to leave it for a few days!
I ran into the problem of not being able to write ID3v2 tags because APE tags were present too, and if it was not for this post I may still be wondering hat was going wrong. I find mp3tag is too quick to report that operations have successfully completed when in fact they have not (similar problem with the leading zeros on WMA files). If is obviously a known issue so can't something be done about it (If nothing else a message thats says remove APE tags first).