OK, you shouldn't open the script with the Perl executable because then it is trying to run where the Perl executable is located, which is likely to be somewhere that you don't have write access for (unless you are using the portable version of Strawberry Perl). It's similar to why we advise against double-clicking the scripts; if a user want to double-click, they should double-click the links in "C:\Users\USERNAME\Documents\bin" because they should have write access there.
The recommended way is to open the Command Prompt e.g. right click the Start button, select Run and type cmd.exe. Alternatively, download the new Windows Terminal program from the Microsoft Store, open and select "Command Prompt" from drop down menu (the "V" button). Navigate to where your input files are with the "cd" command and then type "run_alphamelts.command", with or w/o some command line switches.
Slightly different but related issues came up a few times recently (off the forum) e.g. a user was wondering why they couldn't "cd" when they opened the command line. As it remains relevant for alphaMELTS 2 also, I'm marking it as a FAQ.
Note: you do need use the Perl executable to open install.command, but only the first time you install it. After that the .command extension gets associated with Perl and you do not need to explicitly open Perl. (You would only need to repeat this process if the location of your Perl installation moves e.g. you are using the MATLAB version and you upgrade MATLAB to a later release.)
Hope that helps,
Paula