It sounds like the OF (Original Firmware) is setting the "Music" folder to hidden - it does this every time you use the OF, so you have two choices:
1) Remember to set the folder attributes so that it is no longer hidden.
2) Use Rockbox's native USB mode, which runs when you plug your Sansa into your computer *after* it's already within Rockbox.
You might also want to set Settings > General Settings > Database > Auto Update to Yes so that the Rockbox database contains all the files that are still on the Sansa.