It's a good thought and thanks (you too @JMichaelTX) !
But I've tried that. The dialog is definitely in its front/active state.
I wouldn't be surprised if the cause is related to this though. As in: The buttons think (for reasons related to their parent window's state) that they should present as being in their in the background state.
The KM Prompt windows below to the KM Engine -- so they don't really have a "parent window". But if you mean the app that is frontmost when you trigger the macro with the Prompt, then that might affect it if you in some way activated the app AFTER displaying the prompt.
For example, if I display the Prompt, then trigger LaunchBar, its prompt has focus, and the KM Prompt then does NOT color its buttons:
Since it affects Alerts as well, I'd guess it is a system or a memory corruption issue. Try the usual fixes - restarting Keyboard Maestro Engine or restarting your system.
After that Safe Boot would be the next thing to try.
As I mentioned above, I have Default Folder installed, but quitting that didn't help.
From what I remember (and maybe I'm wrong), nothing on the system has changed in a while. The newest update was Keyboard Maestro, to 9.0.6. Which is why I thought maybe something changed there and as interacting in a funny way with 10.11.6.
I have a backup of 9.0.5 (and earlier), but was hesitant to try them because I didn't want to corrupt the preferences.
Would it be safe (and worth it) to swap out these minor versions of "Keyboard Maestro.app"
A safe way to do this without risking 9.0.6 or later is to
while keeping 9.0.6 around, install 9.0.5 (or earlier) but do not launch it;
create a new user account and log in to that user account;
open 9.0.5 from within the new user account to test its button-appearance behavior.
When testing is complete, log back in to your original user account to delete the user account created for testing. All that will remain of KM 9.0.5 is the app shown in the Finder and that can be safely moved to the Trash. KM 9.0.6 and any of its associated files should remain perfectly intact.
Just tried it now, upon reading your post and thinking the prior versions might be available from the Keyboard Maestro site (they are). Both 9.0.4 and 9.0.5 showed the OK button highlighted.
It appears to be a bug in recent versions of Xcode, when it compiles the interface files for those windows, it has made some change that results in the failure to display correctly in older versions of OSX.
I have reported it to Apple, but there isn't anything I can do directly, since reverting to using older versions of Xcode is not really practical.
Since Xcode supports setting the Deployment target for the interface, and it is configured for 10.11, which it claims to still support, yes they might. It really depends on why it is failing and what it is doing wrong - it is quite possible the bug could affect other things, and until they know what it is doing and why, they won't know whether there are other potential consequences. And once they do, it may be an easy fix. Or not. Or they may not care. Who knows?