It might not be related to your issues, but in my case, I notice the following behavour:
If I launch a homebrew emulator with a channel forwarder from my usb drive, than that emulator is unable to remount my usb drive.
If I reload the running ios, it can initialise the usb drive fine.
If the emulator is loaded from the sd card, it works without reloading the ios as well.
Team Twizzers also had other problems with the homebrew channel if they didn't reload the ios to keek ahbprot.
For that reason, they changed the behavour in the latest hbc, so that it always reloads the ios before launching the homebrew.
The only occasion reloading an ios is not needed is when you are in neek2o environment.
It takes almost 9 seconds there to reload the ios, so it's better not to reload. Since usb access is handeled by arm code there, the
drive remains mounted when you switch from one application to another.