I convert my wave files to flac using custom encoding settings in the converter component of foobar2k. In this step I want foobar2k to include the front cover on-the-fly. Therefore I need to use tags for the --picture option of the flac encoder.
The following screenshot shows my setup. This setup works for me.
Sorry, I forgot some examples of my filenames:
Alexisonfire - 2006 - Crisis.jpg
Alexisonfire - 2006 - Crisis.cue
Alexisonfire - 2006 - Crisis.wav