This is technically speaking more of a question for the
freemyipod team, as Rockbox is classed as
'unusable' by the Rockbox project (no supported bootloader installation method).
Here's the problem in a nutshell:
USB in recent builds of Rockbox is buggy on certain Windows machines (for entirely unknown reasons).
Because of this, the current emCORE release ships with a "fallback image", which is a stripped down version of Rockbox with known working USB - it was this fallback image that enabled you to install Rockbox on your device using Rockbox Utility.
This fallback image can be accessed from emCORE main menu -> Tools -> Run Rockbox fallback image.
You will need to use this fallback image whenever you want to mount the device storage.
The freemyipod team is working diligently in the background to provide a(nother) workaround for this issue, by way of their own "Disk Mode" emCORE application that will be shipped out to the public in the form of a new emCORE release after rounds of testing.
If you were to ask nicely in their IRC channel, I am certain they would be willing to provide you with an updated binary for the purposes of testing.
There are also other things that would negate this issue in the course of further development that haven't yet eventuated - so stay tuned.
[Saint]