Error: difference between Multiple Image Processor and Batch>Macro?

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Error: difference between Multiple Image Processor and Batch>Macro?

KKline
Hi all, I'm new to ImageJ, and I'm running into an issue with my macro.
When I run this with the Multiple Image Processor, the output is 8-bit RGB
Stack images, rather than 8-bit RGB merged pictures; the measurements are
performed only on (i think) the red layer; and the thresholding is not
performed at at all.
When I run the same macro with Batch>Macro function, the output appears to
be what i'm looking for (although now i don't trust the output)...
My question is, what is the difference between Multiple Image Processing and
the Batch>Macro function Why might the MIP be mishandling the macro?

Thanks!
-------------
setBatchMode(true);
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
run("RGB Color");
run("8-bit");
run("Specify...", "width=640 height=512 x=640 y=512 centered");
name = getTitle()
run("Duplicate...", "title=&name");
setThreshold(127,255);
//run("Threshold...");
run("Set Measurements...", "area mean standard min area_fraction display
redirect=None decimal=3");
run("Measure");
selectWindow("Results");
setBatchMode(false);
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