I believe now that the double-spacing is a function of the proprietary platform I'm using. The capping of the second word occurs wherever I use it, though, in Word, etc.
I've played around with using @KEY functions with backspacing, left arrow, ad nauseam, and still can't get anything to stop the capping. If you do figure something out, please do report back! :)
Entries just set up basically (originally) as:
ecoli= E. coli
cdif= C. diff
cdiff = C. difficile
Which work *perfectly* in Word autocorrect. But not with Shorthand.