i have the same problem. i might have identified the problem though. i'm running win7 pro x64 and FoFiX-v3.121-Final-Setup-(py2.6-ogl3). fofix is installed in d:\fofix.
i set my setlist folder to d:\abc\def\ghi\ and put the song into the subfolder jkl\mno\pqr\[song_folder], so the path to the album.png is D:\abc\def\ghi\jkl\mno\pqr\[song_folder]\album.png.
fofix though will search for the album.png in
this only affects the album.png and label.png in the [song_folder]. everything else is searched for correctly (including the label.png for the folders jkl, mno and pqr) and it does not seem to be affected by the theme.
this is obviously a bug, where should i post it? but i'm not willing to create a google account to make a bug report. so if someone wants to, plz do so.