is there any way to make foobar not recognize cue files? often times I have large stacks of ape's and flac's to convert to mp3, and the cue files make it difficult

You could try using the "run convertion, single file output"?

In preferences:

"Core -> Restrict incoming files to:" and add a list of filetypes like

*.mpc;*.ape;*.flac;*.mp3

ah, thank you