Sid
I've done some research on this issue and I can't come up with anything to suggest that flac.exe or flac frontend can't run properly on Windows ME. I think we need to further explore the possibility that there is a flaw in how you have it all set up before we can conclude that it's the operating system.

So I have a couple of questions:

1. How did you install flac frontend? Specifically what version and install method did you use? There are more than one.

2. Are you using the very latest flac.exe and metaflac.exe?

3. Flac Frontend works by producing a batch file (usually called go.bat) then running the batch file. Go.bat remains saved inside your flac frontend directory until the next time you click GO. Could you try to run flac frontend again on a set of wave files that give you errors, then before you do anything, provide us with a copy of the contents of go.bat?