A couple of things...
Your window and it's contents (including your progress indicator) normally do not redraw while you're within a handler. So chances are that the progress indicator is not getting redrawn until you exit the awakeFromNib handler... at which time your progress indicator has already been incremented to it's max value and so it would redraw as already full.
So, one option is to insert calls to tell your window to redraw after each update. But progress indicators have the ability to update themselves on a background thread. So, in this case, an easier option might be to tell your progress indicator to use threaded animation. So try inserting this at the top of your routine:
myProgressBar's setUsesThreadedAnimation_(true)
Another thing is that the "do shell script..." calls that you're doing are probably happening very quickly since all you're doing is a call to "mkdir". So even after adding the above line of code you may not see much if any difference in how quickly the progress indicator fills up.
You might try adding a small "sleep" to each do shell script call to slow things down a little. For example, for each of your shell script calls you could do something like this:
Change this:
do shell script "mkdir ~/Desktop/dir1"
To this:
do shell script "mkdir ~/Desktop/dir1 ; sleep 0.5"
That will add a half second delay to each shell script call and possibly allow you to see the progress indicator fill up more slowly.
Steve