I'm working on a song that features double stops above the 19th fret (at the 21st and 24th fret). EoF doesn't like assigning fret hand positions above the 19th, so what is the workaround to insure proper fret positioning? 

If you disable Rocksmith 1 export, EOF will allow you to use fret hand positions as high as 21 (if there's no capo in use and the track's fret limit isn't lower than 21).

As far as I can tell, that option is already disabled. The option to save as a separate Rocksmith 1 file is disabled, as is the option to export chord techniques from Rocksmith 1. Is there a further option I need to disable?

Not that I know of. I turned off RS1 export, set the fret limit to 21 in a project and EOF allowed me to add a fret hand position of 21 and it saved to XML. You'll need to be using at least r1345 though (RC10 is too old), as that's when I added the ability to use a position higher than 19.

Well there was my problem. I haven't updated EoF in quite some time, and apparently I needed to update the latest build.