I have one specific advice for you: build the utility ffmpeg.exe and give it the command-line arguments like
ffmpeg -i someInputFile.wav outputFile.aac
Run it under the debugger and see what happens. This is a great library and utility, but it's very big and have some legacy "noise" in it, due to multiple patches and updates. Maybe there are some error conditions which are simply ignored, or just the warning is issued and the condition itself is unavoidable or depends on input, something like that.
—SA