iPad TV Episodes not in order?

Anyone else having this issue on their iPad?

I run my TV shows through a program on the Mac called iDentify which adds matadata have been using it for a while but since iOS 7 when I add the TV episodes to iTunes they are all in order by episode number but when I sync them to the iPad they aren't ordered by episode number anymore.

I removed the TV shows from the iPad then added them again and they were in order by episode but then if I go to add a new episode into iTunes then resync they are back out of order again.

Anyone know a fix for this? Not sure why it has suddenly started happening when it used to order then by episode number no problem.