Hal, There is a problem with 2.3 custom themes that has had to be carried over to 2.4 and may not be fixed until 2.5 the way things are panning out at the moment, but I am hopeful it will be fixed before then. However is it being tracked in Moodle Tracker and developers are planning on starting work on it in the new year.
The reason the blocks fall off the page is more likely the way the custom blocks have been coded, it's all in the syntax, and this was not made as clear as it should have been. If I find some time today, I'll take a look at this theme and rework the layouts for you which should help. In the mean time, try using Standard theme to edit.
Cheers
Mary