Oops! From what I could find out the OP's original code was correct. I didn't find any examples of how to send multiple files to flac.exe other then iterating a directory.
Indeed.
This suggestion from the FAQ, in answer to the question "why don't wildcards work?"...
for %F in (*.wav) do flac "%F"
That is a command line example - double up the % signs if including in a batch.
This implies that flac can only do 1 input file at a time, and that the answer to the OP's question, which was...
Problem is, each file was being sent one at a time. I need to find a way to send all the files in the directory to the program at once.
...is, "Sorry, there isn't a way to do that, because flac.exe won't accept multiple file names"
I'd be interested to know why the OP wants to send multiple filenames all at once to flac.exe, since even if it could accept them, it would still process them one after the other, and the result would be exactly the same as the solutions outlined above.