I've noticed strange thing with JUCE standalone programs on Windows (JUCE demo for example) - JUCE versions 3.1 and 3.2.
I can reproduce it with my standalone app as well.
When program starts, it doesn't display its window at the top of other windows . Instead, its blinking icon appears in the status line. Click on the icon puts the window to the front and program works normally. Like program would be put in the background when started ?!?
In very rare cases program starts normally, but icon is blinking nevertheless - setting Shortcut's "Run" option has no effect on this behaviour.
Windows 7 x64 here.