Strictly it takes two when set to record from epg records twice once from bbc2 and once from bbc2 ni, this causes a conflict. A workaround is to record it in hd.
Yes, I was getting a similar problem with “Homes Under The Hammer”, BBC1, some months ago. Set the SD version to record, then when asked if I wanted HD replied “yes”. Ended up getting both SD and HD. Solution was to cancel record and then start from the HD version.