so it is the sync between your computer and the cloud which causes the clash?
Maybe you could try to interrupt the sync after the first 100 books have synced, and then try again. I had that problem with a previous version, and I suspected it was too much to sync for my machine (same on the reader when syncing over WIFI). I have used 3.6.0 for sevelar syncs yesaterday without problems (on windows 8).
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