I pinpointed Dolphin version 10344, which was an update for libusb passthrough, as the culprit for killing USB passthrough on RB instruments. I am aware that there have been some issues and fixes recently for USB passthrough, but it still affects RB instruments on the most recent Dolphin version. Not only that, but RB3 (which is the only one I've tested, but most likely all titles) suffers major frame drops from version 10344 onwards.
We ended up having to drop usbdk support due to issues it was having in Dolphin, are you using that? Can you give any more information on the framedrops? That game lags a lot when trying to connect online since Dolphin doesn't support the asynchronous requests.
Can you try using the latest development builds and libusbK for instruments?
The game simply lags a lot more than it used to before that version. I installed Zadig and replaced the driver for my keyboard dongle to libusbK and it still isn't recognized by the game.