OK, I've tried to change JBPatch configuration options on my PW (5.3.3) for the first time ever and think I've hit a bug. I changed the default margin width down to 20 to see what it looked like, hit save, framework restart, hm, too narrow. So I tried boosting it to 30 and resetting the other two to 50 and 70 (making all three margins actually useful for the first time ever). Save, framework restart, why has nothing changed? It's still set to 20/100/150! OK, try hitting reset, save, framework restart. Still no change! What about reset, save, sync, framework restart? Nope, that won't change it either!
On further investigation, it looks like the first change made via the JBPatch GUI writes out (/mnt/us)/opt/jbpatch/com.mobileread.ixtab.patch.margins.txt, but subsequent changes refuse to overwrite it (normally I'd guess due to permissions, but everything on the Kindle runs as root, so that can't be it). If you change it by hand over USB mass storage or usbnet and do a framework restart, things work.