It is possible I've had to much coffee, but it looks like there is a difference in the way FileMaker 13 handles Freeze Window script step when a script with Freeze Window in effect calls a sub script that moves to a different layout on Mac vs. Windows.
i've got a script takes a while to run because it jumps around to many layouts, calls a child script that goes into a loop that resizes zero to many images in containers on child rows to multiple thumbnail sizes and sends each to a web server via FTP, etc. To hide all this activity from the user, I put in a Freeze Window and made sure nothing in any of the child scripts refreshes the window. Works great in OS X 10.10.
Now, running the exact same fmp12 file on Windows 8.1, the window stays frozen as long as the layout change is triggered in the parent script, but when it gets to a called script that changes layouts, even though the calling script has a Freeze Window in effect, it just kind of ignores that fact and unfreezes the window and displays the layout specified in the called child script. So, I put in a Freeze Window in the child (called) script and now the window stays frozen through out the duration of the script in Windows and OS X both.
I'm kind of not surprised that it would be different, seeing how windows are handled quite differently on mac vs. PC.
The FM documentation only covers that a pause/resume script step will force a refresh (any of those in your child script?) as well as a natural refresh when the script is done executing.