I sort of had this problem. I was flodding the forum with questions but no1 really helped. After hours of observation i finally figured out what was happening. I was converting some movies *i have 200+ mkv movies* to mp4. I added them succesfully to itunes and it played fine but when i connected my ipad it didnt sync to it. I checked the Movies and Tv shows tab and everything seemed to be fine but it wasnt syncing to my ipad. Then i converted some movies to MOV. The ipad takes MOV and MP4. But the same thing happened. And it was a mystery to me because i already had 2 movies in the ipad in those same formats and here i was converting movies to the same format and it wasnt syncing to it. And finally i figured it all out. The format is correct. The ipad takes MOV and MP4 but if it isnt in the correct "video codec" which is h.264 it wont sync to the ipad.
Right click on the video file in itunes and click on "get info", then click on i think is "summary" i dont remember *im at work right now and dont have itunes installed* just click on the first tab. Then you will see the video information. There you will see the video format which is either MP4 or MOV AND you'll also see the "VIDEO CODEC" and since your converting it to MP4 your video format will probably be MPEG-4 instead of h.264. If its not in h.264 it WONT sync to the ipad. Use handbreak and use the ipad settings.
