Have you checked the system preferences on your mac?
(General - Appearance)
You're completly right, the color can be changed there. A bit annoying though having to tell all users to choose a darker blue. But anyway, better this than no solution at all. Thanks
Here's an idea...
if the System Preferences is AppleScriptable (which I have not looked into yet), you could create an AppleScript to perform a change and initiate the AppleScript from FileMaker Pro
Even changing text selection colors provides only partial relief, as most of the highlight colors in OS X are on the light side (by intention). In FM12, that's a problem with several of the (otherwise attractive) dark themes, such as Onyx, as they use reversed out (light on dark) text even for editable fields. I've experimented with using dark themes but changing editable fields to dark text on light-colored background, with decent result. It also provides a good clue distiguishing editable from non-editable fields.
I like Mark Scott's suggestion (dark text on light-colored background).
As an elaboration on his idea:
You might try setting the field to use dark text on light-colored background only when the field is in the 'focused' state.
This would allow for preserving the overall look of the layout, except for at the moment where it it might be good to deviate from the general color scheme.
You can actually choose whatever color you want (at least on the OSX Lion machine I've tried). The last box says other... and allows you to choose a darker color.
I like your idea of switching the background and font color in the focused state. I might give it a try....