itunes not transferring most photos

I am trying to figure out a pretty simple problem.

itunes will not transfer all the photos i've selected from my macbook pro to my iPhone 6s.

I don't want to use iCloud as I have more than the free storage worth of photos. I have 20g free on my phone so it's not a device space issue. Especially since these photos were on the phone yesterday before I "upgraded"

I've restarted the apps, the computer, the iPhone, changed cables, changed usb ports.

I've checked sync photos, selected albums, then the selected albums in iTunes and I get less than 25% transferred (4947 selected, 1094 transferred). Most albums are transferred, just without the proper numbers of images according to iTunes. All the photos were synced to my phone prior to the iPhoto to photos app migration. All the photos can be found, used, printed, whathaveyou with the photos app. So they do indeed exist. I've even uploaded one of them to test the iCloud photos feature, which was a huge mistake (now the only way to delete that photo from the cloud is to delete it everywhere). It's an iTunes transfer problem.

I recall this issue in the past, but then it was a iPhoto trash empty or something easy that fixed it. That option is not available with photo.