I had similar problem with my Onyx Prometheus sd card - I have ~26GB of files on it and it took ~5 mins to boot and check the files. It also took forever to connect to PC and disconnect from it.
I've found the solution
here.
You should decide for yourself wether you do it or not, but in my case it solved the problem
Basically:
1. Root the device (KingRoot would do it in 5 minutes).
2. Install any file manager with root priviledges (I used FX + root addon).
3. Go to system/bin folder and rename the file fsck_msdos. I just put zero in the beginning.
4. If you don't need the root, uninstall the KingRoot. But I'd keep it to install useful stuff like Button Savior.
5. Reboot your Onyx.