Hello.
If I understood you correctly, you can't see some files in "database view". So you could try to update the database or rebuild it by initializing it (
http://download.rockbox.org/daily/manual/rockbox-sansae200/rockbox-buildch4.html#x7-480004.2.3), like G4Oblivion suggested, or go to the .rockbox folder on your sansa and delete all *.tcd files in it (should be 10 files, at least on my iPod there are 10) and rebuild the database from scratch (initialize it) afterwards by going to the database settings. This helped me, when changes of some id3 tags of some files didn't apply after updating the database and were not visible in "database view".
If you can't see files/folders that you know that should be there in a directory in "folder view" check your file limit settings (
http://download.rockbox.org/daily/manual/rockbox-sansae200/rockbox-buildch8.html#x11-1400008.5.4) because if you have more files in a folder than the limit set, you will not see some files/folders.
I never used a program like WMP to put files on my player or sync it. I only use drag and drop. Does syncing work in MSC? Shouldn't it be in MTP?
Hope you can solve your problem and keep on enjoying rockbox.
Greetings, c_k.