Last time, I presented a strange problem I was having with runas.exe. I believe I have found the answer:
"Run as different user" sets the startup directory of the new process to the directory that contains the executable. runas.exe, however, always sets the startup directory to System32.
The unexpected current directory confused the program in question, which explains why only "Run as different user" worked. In fact, runas.exe requires a fully-qualified path if the target program is not on the system path, even if launched from the directory containing the EXE.
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