Hi Juan -
i'm not sure if this behavior is only present on the x86_64 version of PI or not; i need to try it on the 32-bit version still. so this might fall under "graphical weirdness" on osx x86_64:
when a script is running, PI just will not stay "lowered". at some point during the execution of the script (batchformatconversion and batchdebayer both cause this), PI comes to the foreground on its own. when using OSX's spaces feature this is particularly annoying because you switch to another space while PI is working and boom, it comes right back to the space that PI is in with PI on top.
i'm still on osx 10.6.3, not sure if this has something to do with it.