Minimized apps re-opening on startup

Am I alone in having this problem or is it not a problem at all but a new 'feature'? I've tried searching Google and these forums, but my queries didn't result in any issues similar to mine.
The problem is with apps that are opened automatically after a reboot (apps that were open when the system was shut down).
Apps that had a window open when the system was shut down, open normally and work fine. Apps that were minimized/had no window open (Skype, for example), do get a marking in the Dock like they are started, but they don't actually start. If I click the Dock icon, then the app is started (no icon bouncing, but I get the screen of Skype signing in, etc...). This seems to happen with every app that opens into the Dock but didn't have a window open when it was shut down.

Aha! Interesting.
(No offense intended with the Windows reference; that was for other readers new to Mac.)
I just tried it, and after restart with no window in iBiz, iBiz was marked as running in the Dock and also appeared in AM, even though I had not clicked on its icon. Although Word had no windows open on restart, after restart it displayed Document Gallery.
The other thing I noticed is that some apps seem to take longer to "recover" after this type of restart. When I did click iBiz icon in Dock, it reopened its default window, but it took 5-10 seconds.
Just out of curiosity, I wonder if the system is just taking longer to "get around" to loading all app components into active processes, if the apps you describe as "not actually started" would eventually start? I noted that Acrobat was initially listed in AM in red as not responding, but eventually it appeared in AM normally.
I note when I click on one or another app's icon after this type of restart, sometimes windows are grayed or take 3-4 seconds to fully load. I suppose it could depend on processor speed, available RAM and number of apps having to re-start. How many apps are indicated in Dock as running for you in this scenario? I have 8 plus Finder, early 2008 Mac Pro with 8GB RAM. I see you have two 120GB SSD (Cool! I'm thinking about adding one).
Sorry, but I can't think of anything else. Perhaps one of the other gurus around here has more insight.

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