It's the "ePub fixed/adjustable top/bottom margins" patch in libnickel that's causing the reader to reboot when opening a book.
And something odd, when I enabled the "Remove recommendations (row1col2) from home screen" in nickel the first time by manually editing each file, it created the KoboRoot.tgz file successfully. For all this testing though I used the kobopatch.yaml to enable all patches, and when using it, it pops up with a fatal error and fails to create the file. Possibly it's not compatible with "Remove footer (row3) and increase cover size on new home screen" and I missed a warning?
These are the patches I enabled, in case there's a conflict between the 2 I'm having problems with that I missed:
I can live without either of those patches, but in case this helps you pin down any issue (or user error is entirely possible too!

... just smack me if that's the case).