I wanted to have the option of keeping both putty.exe and puttytray.exe in my app\putty directory I tried both:
PuTTYExecutable=PUTTYtray.EXE
and
PuTTYExecutable=App\putty\PUTTYtray.EXE
They both caused PuttyPortable.exe to error out saying it could not find putty.exe