Have you checked the box for "Always use this app to open .wpl files"?
It's worth mentioning that Mac OS X Finder does this right, a group of items gets properly delivered to the app without spurious process instances or other issues.
Enqueue missing from M3U isn't related to recent foobar2000 changes or bugs in Windows 10. It is missing by default on Windows 7, 8/8.1 and 10 but works on Windows XP. Somehow Windows Media Player's commands are shown instead of foobar's for this file format.If this is your issue and you don't need WMP it's easy to solve by disabling the program. You can type "computerdefaults.exe" in the Windows search bar and run the program. Click on the Custom line and untick "Enable access to this program" from Windows Media Player.