If memory serves, if you loaded files into the Clip+ with it configured for USB MTP mode you cannot see those files in MSC mode and vice versa. I think people here say the recommended mode is MSC not the default Autodetect. If you pull the microSD card and use a card reader you should be able to see the files on a computer. When it comes to microSD card issues some seem to fix the issues by formatting the microSD card with the SD Formatter 3.1 for SD/SDHC/SDXC program.
You may want to upgrade the Rockbox to the current build. If you have to reboot into the Sandisk firmware for USB transfers then its a good bet you are using a Roxbox release that is release 3.10 or earlier. Roxbox releases newer than 3.10 have the USB enabled. Using the current build on a Clip+ and do not have any trouble with Roxbox working in USB mode to transfer files both to the Clip+ and microSD (16GB) card.
You can use the RockboxUtility to update the Roxbox firmware to the current build. Put the Clip+ into USB MSC mode via the Sansa firmware before upgrading the Rockbox firmware or installing it for the first time.
More info about updating the Clip+ and some known issues can be found at this link:
http://www.rockbox.org/wiki/SansaClip
It might be advisable to start from scratch by booting to the Clip+ Sansa firmware, copying all of your audio files to your computer. Then in the Sansa firmware, format the Clip+. If using a microSD card, remove the card from the Clip+ and format the card with the SD Formatter 3.1 for SD/SDHC/SDXC program. Do not reinsert the microSD card until the Clip+ has been updated with Rockbox. Once the Clip+ has been formatted, in the Sansa firmware configure USB for MSC. Next if the Roxbox firmware has been erased due to the formatting, reinstall it using the RockboxUtility to the latest current Clip+ build. If it hasn’t been erased, update it to the latest current build with the RockboxUtility. Then copy your music back to the Clip+.
