Photo sync when Photoshop Elements also on PC

Hi, I've a really annoying problem with iTunes and Photoshop Elements when syncing photos to my IPod. I use Elements on the PC to manipulate photos, not specifically to organise them as I already have a folder structure that suits my needs. I also use the flatphoto.pl script which allows me to flatten that structure so that individual folders appear as separate albums under Photos and IPhoto on my IPad.
When I sync I specify 'sync photos from'  my parent folder which contains a list of my folders/albums, and then select around sixty other so folders I want synced. As I have around 6000 photos to sync, this takes a long time, so I thought I'd do it over several sessions.
However, when I reload iTunes, it had unpicked the sync photo option, and defaulted to Photoshop Elements rather than my selected parent and sub folders. I then had to individually re-select the folders I wanted synced, but iTunes now thinks the photos on the iPad are from a previous, different sync and wants to delete them.
Why is ITunes changing my selection between reloads and how can I prevent it doing so? As well causing an issue with this initial sync, I can't see how I could then later add another folder even if I let first sync run to completion over almost a day I'd guess.
I'm on Windows 7, ITunes 11.0.5.5. I've googled this extensively and can't see the issue described as I experience it. Hope someone can suggest a way round, hopefully short of ditching what I have and going for a third party app....

Hi, I've a really annoying problem with iTunes and Photoshop Elements when syncing photos to my IPod. I use Elements on the PC to manipulate photos, not specifically to organise them as I already have a folder structure that suits my needs. I also use the flatphoto.pl script which allows me to flatten that structure so that individual folders appear as separate albums under Photos and IPhoto on my IPad.
When I sync I specify 'sync photos from'  my parent folder which contains a list of my folders/albums, and then select around sixty other so folders I want synced. As I have around 6000 photos to sync, this takes a long time, so I thought I'd do it over several sessions.
However, when I reload iTunes, it had unpicked the sync photo option, and defaulted to Photoshop Elements rather than my selected parent and sub folders. I then had to individually re-select the folders I wanted synced, but iTunes now thinks the photos on the iPad are from a previous, different sync and wants to delete them.
Why is ITunes changing my selection between reloads and how can I prevent it doing so? As well causing an issue with this initial sync, I can't see how I could then later add another folder even if I let first sync run to completion over almost a day I'd guess.
I'm on Windows 7, ITunes 11.0.5.5. I've googled this extensively and can't see the issue described as I experience it. Hope someone can suggest a way round, hopefully short of ditching what I have and going for a third party app....

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