First, when you do a straight upload without the sync option you won't be able to synchronise that tree with your FTM tree. You would have to do another upload with the sync option to a BRAND NEW TREE.
Second, if you can't just do a straight upload I would see if the log created during the upload can help you identify the parts of your FTM tree that the upload process doesn't like. I would keep escalating this to the support people. Sometimes you get someone knowledgeable who can help you. Other times ...
Have you created a small test tree, to see if you can upload this? If that works then it is most likely something in your FTM file. If it doesn't work then it is more likely the FTM installation or something else on your system that is interfering with the process.
Sorry I can't be of more help.