When I tell the Parallels application to hide, I expect it to hide completely. This has been bugging me for quite a while -- it's been present since 1940 in one form or another. Here's how to reproduce it: 1) Open Parallels 2) Start guest OS 3) Hide Parallels 4) When guest OS changes resolution from it's boot loader to its defined resolution, Parallels unhides itself and puts itself into focus 5) Hide Parallels 6) Not sure what the next trigger is, but something once again makes Parallels unhide itself and brings it into focus 7) Hide Parallels 8) Again, something once again triggers Parallels to unhide itself and brings it into focus So, after the initial hiding of Parallels, it inexcusably steals focus at least two times before the guest OS has finished loading. Very annoying!
This happens also when any Windows application opens up a new window, or a balloon pops up from the Windows Task bar. It is incredibly annoying. Though Parallels cannot prevent Windows programs from poping up a new window when you are using Windows - that's the normal operation for Windows. Parallels should be able to control whether such action causes focus to be taken away from a Mac OS app.
Check what is getting loaded as Windows starts. A native way to do that is using MSCONFIG.EXE although there are lots of 3rd party apps as well. I suspect that the culprits are the programs that are invoked when you start up Windows
