OK, well, this "damage control team" problem is a strange one. It turns out it has nothing to do with the CSV files. I thought the problem wasn't appearing in stock until I remembered that I had left the stock batch file at 1024x768. When I changed it to 1440x900, it evidenced the exact same behaviour. There is a bug in the script itself for that resolution.
I don't know Perl and I don't have a runtime installed on my computer, so it's a bit hard for me to debug. Nevertheless, I have a powerful suspicion that the script is going awry in the MouseMoveAbsPix subroutine. It enters an until() loop on line 811, and I think the condition never evaluates true.
But why it's happening, why I've only seen it triggered with this one command, I have no idea. It's possible that it occurs with other commands as well. I probably haven't used every single command defined. Another command with the same co-ordinates ("Aim For Weapons", ID=543) works fine.
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