The issues you're seeing are probably a result of old auto-import rules not working correctly after the migration. Specifically, try:
1) Export Linux/Id Library and Import the library on Windows
2) Quickly turn off auto-import in the background under options
3) Use the "rename, move, copy" tool with the Update Path option to fix the file paths and direction of the slashes. Specifically replace the root of the Linux filesystem with your drive letter (C: or D:, etc.) and check the box to reverse the direction of slashes. Try a few files to test, then you can do the rest all at once.
4) Write down your auto import rules (if you need to), and then delete all your old auto import rules
5) Re-create the auto-import rules with the correct paths
6) Close JRiver and check the Platform.jmd file under your JRiver library directory to make sure that it says Windows rather than Linux (do not skip as a library restore may have undone this step!)
7) Restart JRiver
8 ) Turn auto import back on.
If you follow these steps correctly, you'll have all the same library info as you used to have and there should be no phantom auto-import problems.
This is based on reversing the steps for a successful migration from Windows To Linux from here:
https://yabb.jriver.com/interact/index.php/topic,128397.msg890849.html#msg890849