Script "blocks" certain applications

I'm running a script that runs from 15 minutes to an hour (or more).
Many applications (web browser, office applications etc.) work fine while the script is running.
(I'm using Windows 7/64)
The script creates 50-200 indd files, and pdf files of these.
But, one of the programs I use most, UltraEdit is "blocked" (not responding)..
Windows Explorer is also "problematic",sometimes I can use it, sometimes its reacting slow (and not responding)..
(It works perfectly when the script is not running)
Anyone else have similar experiences? Any solutions?

This is new ... got this attempting to do *anything* else while running quite an extensive ID javascript. Seems my system is lacking the jajaja to handle two jobs at a time.
(Oh boy was I tempted to select 'restart', just to see what happens next! Instead, I chose to count my fingers until the computer got responsive again.)

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