今更ですが……
どうやら CRT の _spawnlp, _spawnvp がエラーを出すようです。
また \write18 も同じ状況でエラーになるようです。
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C:\work>PATH=C:\texlive\2019\bin\win32;C:\WINDOWS\system32;C:\WINDOWS
C:\work>ptex \relax
This is pTeX, Version 3.14159265-p3.8.2 (utf8.sjis) (TeX Live 2019/W32TeX) (preloaded format=ptex)
restricted \write18 enabled.
*\immediate\write18{extractbb --version}
This is extractbb Version 20191114
Copyright (C) 2008-2019 by Jin-Hwan Cho and Matthias Franz
This is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
*\bye
No pages of output.
Transcript written on texput.log.
C:\work>PATH=C:\C:;C:\texlive\2019\bin\win32;C:\WINDOWS\system32;C:\WINDOWS
C:\work>ptex \relax
This is pTeX, Version 3.14159265-p3.8.2 (utf8.sjis) (TeX Live 2019/W32TeX) (preloaded format=ptex)
restricted \write18 enabled.
*\immediate\write18{extractbb --version}
system returned with code -1
*\bye
No pages of output.
Transcript written on texput.log.
C:\work>
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他の TeX 関連ツールのシェルコマンド実行機能でも発生するかもしれません。
一方、 \input "|command" は正常に動作するようです。