However, I have not tested for doing another screen shot before you have finished the macro of the current screen shot. I don't know why that would every happen. As soon as you complete a screen shot, the macro immediately pops up.
But maybe I'm missing something.
Yes, you are 
Itâs not the user who is making two subsequent screenshots, itâs the OS that is placing two files in the Desktop folder. The first one you donât see. Itâs the temporary dot file (see my post above and/or the screenshot here). This triggers the first run of the macro. You wonât see the user prompt, because the macro gets stopped at the ^Screenshot condition.
A little bit later (how much later depends on the size of the screenshot) the final file âwithout dotâ appears on the Desktop. This triggers the macro again.
Run the macro in debugging mode (Keyboard Maestro Menu > Start Debugging) and youâll see the two instances of the macro. Or remove the file name condition, and youâll see two user prompts. If you donât see it, than the whole thing is something new of El Capitan.
Note that I did not have to add any of these:
Pause before the variable declaration
a Semaphore Lock action
It seems your new version runs fine so far, even with small screenshots. But, as said, the whole thing seems to be a timing issue between the first and the second instance of the macro. Since you inverted the file name condition (!^Screenshot) in the new version you may have âaccidentallyâ resolved the issue. But when the macro is run on a different machine (faster or slower CPU/disk) I wouldnât bet that the issue wonât appear.
With the Semaphore Lock you are on the sure side, since it doesnât let run the second instance unless the first one (the one from the dot file) has terminated.