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You can try setting width and height on the thumbnail img tags, maybe when fancygallery runs before the images are loaded it reads their width and height as 0 and tries to position them in the middle of the gallery boxes… not sure if that’s your problem though, didn’t really dig into it.
adding the didn’t work… I did find out that line 17 in the “jquery-fancygallery-1.1.min.js” file is an area w/an area that manipulates the boxes and colour and sizes… but can not find the placement issues…
I played with this file but still can not find the area of placement…
This way you would know exactly how each element in your layout would behave.