I posted the following on bleepingcomputer. Another friend suggested me to post here...
"It seems to me I've had this problem pretty much since I installed Windows 7 on this new computer. A friend of mine suggested me to ask help from here.
Some programs start up minimized most of the time - but not always. At least Mozilla Thunderbird and Adobe Premiere Pro CS5 keep doing that to name a few. The shortcut properties have "Run" as "Normal window" for both programs. I think I've also tried closing them with Ctrl pressed as suggested somewhere.
As for other similar problems, I get occasional problems with opening windows from the taskbar groups. The window shows up nicely when hovering over the thumbnail picture of the taskbar group, but when I select it, it just flashes on the top and then disappears / goes back behind other windows. Alt-tabbing seems to work flawlessly, but it'd be nice to be able to use the taskbar too.
Any help appreciated. Let me know if you need further info... "
I've noticed later that Alt-Tabbing doesn't work always either.
They suggested me to try and pin software to taskbar at bleepingcomputer. Both Thunderbird and Premiere have started normally when launched with the pinned icon instead of the desktop shortcuts. That's not the real solution though and the problem remains at least with Windows Media Player. It goes often minimized when launched by double clicking a video file on explorer.
I did a search on your site and found Toasty's post (Programs start Minimized, will *NOT* maximize.). Also it said in some post that you should press Alt when closing. I'll try that next time the problem occurs, but I doubt it's the solution as the programs sometimes open normally and sometimes don't. Either way there's also the problem with the taskbar...
Thanks in advance. It's really annoying when I can't rely on such basic functionality with my shining new OS.