iPad air sync problem

[Gozoman Island Lover]

When I connect my iPhone6s up to my laptop and enter iTunes, and then click on my iPhone6 and photos I get the option to sync all my photos. I can select my pictures and then select the folders I want to sync. I have always did the same with my iPad Air as I had it set up the same however when I connected it up the other night for some reason it deleted all my photos off the iPad. When I click on photos, and select sync photos, then select copy photos from and select choose folder this is where the problem starts. If I click on my pictures and then click select folder I get a message stating, You have selected a library, please select a folder instead. I have no option to click on individual folders as I do with the iPhone. Below the Sync photos window 'All folders' is selected and I don't have the option to put a tick in 'selected folders' as it is greyed out. I can only click on one folder to copy. If I copy that folder and then repeat the process to copy another folder it deletes the one I have already copied! This is driving me nuts! The only change I have made on the iPad since I last synced it is that I installed software for a flash drive called iShuttle from Integral. Could this have screwed things up in some way or any other ideas how to get my syncs back to normal?