PaladinBL
Did you see the: "Experimental,
affects only books opened afterwards" comment in addon's settings?

"Continue reading" doesn't count (unless it was right after reboot, and you've changed settings before going into "continue reading")
And, as I said, you just give files .css extension and don't name then "style.css", but other than that, you can use any name and have as many files as you want:
myCoolStyleWithItalicFonts.css
helvetica_noMargings.css
whatever.css
regarding corrupted file system, it's important to know:
1) Due to the nature of flash based FS, changes to one file could affect many
2) The best way is to use "safely remove hardware" option in windows (there should be similar options in other OSses), in the worst case, wait at least 5-8 seconds after saving changes
Did you try to reset the reader?
VICTORSJG
prsp.sh was changed, 2 new folders /opt/mnt/ms /opt/mnt/sd were created.
Fsk image is created by an ant script, available in "build" repository.
I don't know why it is smaller, maybe because prsp.sh has become smaller.