I find that sometimes if i overwrite the .rockbox directory directly (this is via USB by the way) i get problems in rockbox. It's probably safer to rename the copy on the microsd card to something like ._rockbox, copy it all over (so you have two copies in parallel) then rename the directories.
e.g.
rename .rockbox -> old.rockbox
rename ._rockbox -> .rockbox
Then you effectively have a virgin install which is far more likely to work than an overwritten one, and you still have the previous install on the sansa so you can copy over themes and settings to the new install.