Resource Import - importing data which doesn't exist

I'm working on importing a 1000 line spreadsheet of resources / accounts. Each resource has ~10 accounts under it which are all unique. I've got 6 fields I'm importing: Resource, Department, Client (custom added field), Group (custom added field), Username, and Password.

When I do the import I end up with about 200 extra passwords in the system - it looks like there is a problem with the custom added fields being imported properly as I see custom fields which do not have the right values. I've checked the CSV file by hand and it is correct - they are very clearly being imported wrong by the application.

Is this a known issue and is there a fix?

Thanks,

Dan