hmm
for one, make sure in options>general you have "update tags when file info changes" checked ON
if you didn't use MC to convert, and you imported the FLAC, you'll need to make sure tools>import>configure>"write file tags..." is checked ON
try selecting all the files and right click>cover art>quick find in file or directory (if there is a folder.jpg, it will find it)
did you convert the FLAC into separate folders? did you use the RMC tool to move them?
the RMC tool can be a bit tricky and so can the cover art...i learned long ago to make an "incoming" folder that ONLY looks at the audio files (nothing else, no cue or log or jpg or anything). This way, when you use RMC it will move all of the ancillary files properly
also i don't convert a lot of files, but when i do i always convert to the original folder, then do the moving with the RMC tool. this ensures i have everything set correctly, i'm always paranoid so i want full control over what is going where
sorry probably not much help...hopefully a bunch will show up with the quick find and leave you with a little less to deal with.