<span class="fp fp-de"></span> <span class="fp fp-md fp-de"></span> <span class="fp fp-lg fp-de"></span>
<span class="fp fp-md"></span> <span class="fp fp-md fp-md"></span> <span class="fp fp-lg fp-md"></span>
So I suggest to use either a different suffix for the medium size or set the default prefix to a different value.
Also, a quick workaround for the first problem would be to move "md" to the beginning of the default $fp-countries list so that any other flag classes can overwrite the background-image property since the classes are defined later in the resulting css file.
(I'm aware that it's possible to change the value for $fp-prefix manually, but I still think the default config should make sense.)