I've been having some really random issues with beat sync. It seems to happen on certain songs on certain USB exports, but it's not consistent and it changes depending on the export. If I reboot the XDJ and go back to the two songs I'm mixing it seems to work fine (but obviously I can't do this in the middle of a set!).
Here's a video of the issue in action (excuse my language!)
I would suspect that the first USB drive you used had an issue where you may have made changes to either the song or the grid and it wasn't updated properly... and what @George said can apply as well -- low quality USB drives are worth avoiding.
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not seen anything like that before, but I would suggest seeking and buying a better/faster usb sticks, the ones you're using look pretty low spec. I use these and they're very reliable and work consistantly well: https://www.amazon.com.au/Kingston-Data-Traveller-64GB-DTSE9G2/dp/B00SOL9Z1M/ref=pd_sim_201_2?_encoding=UTF8&pd_rd_i=B00SOL9Z1M&pd_rd_r=e0f14e69-b10a-11e8-91f0-930b69d3e606&pd_rd_w=WaCTK&pd_rd_wg=wD6zW&pf_rd_i=desktop-dp-sims&pf_rd_m=ANEGB3WVEVKZB&pf_rd_p=099d9e8c-2145-4a01-aed2-8f1176c32667&pf_rd_r=WM8THNHAF0BEHFQ6443G&pf_rd_s=desktop-dp-sims&pf_rd_t=40701&psc=1&refRID=WM8THNHAF0BEHFQ6443G
George UK