signtool fail with inno setup : 0x80070003 - "Store IsDiskFile() failed"

I figured out the problem, the path to the certificate must be relative to the installer output path, not the current working folder. In this case, it would be "..\cert.pfx".

I had the same problem. My problem was I have used " in the signTool command, while I needed to use $q instead. Surprisingly it was successfully signed the executable but it failed to sign the result setup.exe file.