Apparently the default Mac OS X Firefox theme is squishing the icons a little bit. The different OSes have varying theme characteristics in the current version of Firefox. This is a pain in the ass for development, especially because I don’t own a Mac. I had about 200 beta testers for a month or so, but nobody noticed the subtle issue. I’m looking into a way to fix it at the moment.
Some people also do not like the light flag border when using a dark theme. I tested this before the release and thought it looked OK, but I don’t use dark themes personally. The 5.0.1 update has an updated border that will use a dark border under dark themes, so it will be less noticeable.
Also previously noted is that if you use a lightweight theme (wallpaper/skin/Persona) under Linux (or possibly some other OSes, but not Windows) then Firefox applies an unfocused effect to your interface. If you click the address bar and the flag icon gets lighter, it’s because of your theme. Under Windows this only affects the background and not the icon. There is no way to override this effect for just Flagfox; it affects everything, including search plugin icons. I was well aware of this effect before the release, as I am on Linux myself, however I don’t personally have an issue with it. If you do, you can disable it with the following userChrome.css:
#urlbar:-moz-lwtheme:not([focused="true"]),
.searchbar-textbox:-moz-lwtheme:not([focused="true"]) {
opacity: 1 !important;
}
Update:
A fix for the border issue has been released in Flagfox 5.0.1.
Flagfox 
From your latest, “Apparently the default Mac OS X Firefox theme is squishing the icons a little bit.”
What 1 pixel? These people need to get a life. I’m on OSX and I actually reduced the icon to
max-width: 22px
using userChrome.css to provide a little more room in the URL bar.
You are doing an outstanding job and need to ignore the outliers. Pretend you are reading Amazon customer reviews where you know 10% are worthless; those 10% complain about everything.
I’m aware I shouldn’t listen to the ones who declare themselves to be the only opinion because they’re loud. Still hard though. 😉
That being said, someone gave me a screenshot of a specific issue on Mac. (a light discoloration of the bottom of one flag indicating that some flags are being downsized under certain issues when they shouldn’t be and that on some systems this downsampling is not working correctly) It doesn’t look like it’s supposed to and I’m looking into it at the moment. I don’t own a Mac so I can only test under Linux and Windows, where it looks correct. The variance in themes between OSes is a major pain for addon development. It will be a wonderful change when Australis hits release and Mozilla actually has consistency in its theming. (though, the address bar focus issue remains; I’ve reported this to them as a bug)