Not sure if this is a problem because of Jaikoz or Musicbee, but i’d say the problem lies with Musicbee. Thought i’d mention it here as well https://getmusicbee.com/forum/index.php?topic=30648.0
The way Copy and Paste/Drag n Drop work is the items copied or dragged present themselves as different flavours (data types), so for example an image could present itself as Image, File or Url , then as long as the other application understands how to deal with at least one of the flavours it can complete the paste/drop.
So maybe MusicBee has changed the data flavours presented to Jaikoz, and there is no longer a flavour that Jaikoz understands. Having read your link maybe MusicBee changes the flavours used when you select more than 1000 files ?
I’ve posted your reaction at the Musicbee forum. We’ll see where it goes from there. Not expecting much from it, but at least i gave it one more shot.