Only Syncing parts of tv series and not the whole thing?

I have had Apple Tv for a while now but all of a sudden im starting to get problems.
When i want to sync the whole series of a tv show, it syncs most of the shows but not all of them and in no certain order, for example:
Episodes 1,2,3,6,12,14,18,20 are NOT there but the rest of them are.
I only tick the box for the tv shows that i want to sync to Apple TV in iTunes, that is how i bring them into Apple TV. Is this correct or should i be doing it another way?
What could be the reason it is leaving out episodes ive tried everything i can think of. Ive restarted ATV and carried out a factory reset on ATV i have now just synced to ATV again and the same thing keeps happening but this time it has less episodes than before.
I have plenty of room on the ATV hard drive so i know its not the HD filling up.
Any help would be great, thanks!

Couple of questions for you.
Wifi or ethernet.
Is it the same shows that don't sync every-time.
Are you trying to watch while syncing.
Are you syncing all unwatched episodes or all episodes.
Can you watch the episodes that don't sync by streaming.
Are these purchased shows.
I wouldn't be worried that they don't sync in episode order.

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