Malcolm,
Would you be able to share a minimal script + swf that demonstrates the problem? Then I could load it on my various test setups and see if there's a pattern.
Super-hacky workaround idea: one might be able to set up an onKeyPress event listener at the HTML level, and then pass the captured enter key to flash via javascript. (What I don't remember is if the window even receives key presses when focus is on the Flash movie...)
Cheers,