If desperate, you might try using IPC::Open3 or IPC::Open2 or IPC::Run or Capture::Tiny or IPC::Capture - they may give you more or different diagnostics/results to what you are currently seeing, and trigger an aha moment. Disclaimer: I've not used these myself, just throwing them out there in case you think it's worth a shot.

See also: Suffering from Buffering by mjd.