I played around with different USB devices and was able to reproduce this bug that nintendont randomly gets stuck while checking FS. It seems that nintendont is hanging in exactly this line:
https://code.google.com/p/nintendon-t/source/browse/trunk/kernel/main.c#123
which means that it is stuck in the function f_open, which is a function of FatFS. This probably means your device isn't compatible with FatFS. I have a few USB devices which have this problem, but most of my devices work fine. So the best solution is to try another device. However, if you ALWAYS stuck on checking FS, then probably your filesystem is wrong and you have to reformat your drive. If someone feels terribly boring he could try to find the line in which f_open gets stuck, the source of FatFS is open. But I don't think this is fixed easy.
Since it is stuck, I don't think there's a way to return to HBC after a certain time. Might be wrong though.