I just delete the cache every time I pop my SD card into my PC. I guess it's old habit of mine with anything that has a cache. I haven't had a issue with it yet though. It would be great if they could add a clean cache option to the firmware. Even if you delete a book from the card it stays in the cache making you have to manually delete it just like the Restore folder.
I can change fonts without problems. The other day I went through all my fonts viewing them in Coolreader then went back to reading without any problem. I love I can have as many fonts I want in CR!
Maybe it's the type of SD Card? I'm using a Sandisk SDHC 8GB.