Using qx or backticks will only capture the STDOUT. I'm wondering if the calls where you are not capturing anything could be related to the "output" of the external command is going to the STDERR instead.
Whenever I have used backticks and I don't get what I expect, a common debugging technique that I use is to store the external command in a variable and print that out. That has helped me find mistakes in constructing the external command that I wanted to run.
One suggestion that you could try is to look at using Capture::Tiny, which will let you capture STDOUT, STDERR and the exit code of an external command.
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