Syncing photos to iPhone after iPhoto crash & rebuild only transfers a few pictures.

I am using an iPhone 4 and iTunes 10.7.  I am running 10.8.2.
My computer crashed while I was using iPhoto - seemed like a kernel panic from what I'm told - and when I restarted I had to rebuild the library.  That went fine (except for a bunch of pictures that I had to re-rotate), but when I synced my iPhone I noticed I suddenly had 4 GB free.  I checked and only 100 pictures or so were on my phone, instead of the usual 4,000. On the iTunes photo syncing page all the albums are displayed, but the numbers of pictures shown next to them are zeros and ones and fours, instead of 230, 81, etc.
I've tried deleting ipod photo cache, repairing permissions and re-rebuilding in iPhoto, making new albums in iPhoto and syncing those.. I don't know what to do!  New albums I just uploaded have the full amount of pictures in iTunes page.  Just to be clear, everything is working normally in iPhoto and on my phone (as far as I know), but something in iTunes isn't seeing many of the pictures is should be. 
Any help is welcome!
Thanks in advance,
Gray

Also, if I edit the photo in iPhoto, iTunes "sees" it then.

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