So far it's just the one project. I've tried another project and it works as it should. I tried to do just one rhythm guitar track and it's still the same; in effect although I'm selecting exactly 8 bars to delete, it's deleting a little bit more.
I have an idea about what's happening:
This project is my second take of the song;I recorded it first at a different tempo, then decided I wanted to change the tempo. So I deleted all the audio take lanes, leaving the tracks empty, changing the tempo, saving it under a new filename, then re-recording the new audio parts at the new tempo. There are no tempo changes in the song; it's been changed through the tempo widget/thingy in the main X3 window.
I think X3 is "remembering" the tempo that the song was first recorded at for the audio tracks and cutting out a size that would have been correct for the original tempo but not for the current tempo.
http://axiology.bandcamp.com