It might be completely unrelated, especially if the OP was encountering this with files built by Amazon/KG/KP, but there was a fix for KF8 output in Calibre a while back to fix weird pagination errors...
It doesn't fit the OP's issue exactly (with the only book I had that suffered from this, the symptoms were a little bit less severe: it was just switching for a little bit more than one page from time to time (or a little bit less, can't remember exactly)), but that might be something similar...
Or not, especially if that happened on mobi6 files
.