Steps: 1. Create a file layer 2. Move it with the transform tool 3. Save and close the file. 4. Reopen the document. The file layer's position has been reset. Also happens if the file layer is in a group and you move the group. The only way to save the file layer's transform is to use a transform mask right now.
Hm... it seems that this is fixed in master. Maybe because it only fixes it because the transform tool is disabled on the file layers, but I cannot reproduce with the move tool, in any case. I will close this now. If you are able to reproduce still, please reopen with a video or something, maybe there's something I am missing.