Apps stuck after Mavericks wake up

I just got a Mac Mini and I wanted the latest software so I installed Mavericks. Whenever I leave my computer alone and go do something with app open, for example Opera or VLC player, the current app is stuck beneath the upper bar! It happens every time after waking the computer up. I have a Dell 2709w (1920x1200), connected via HDMI>DVI because, guess what, if I connect it directly over HDMI I can only use 1920x1080 and not the full res, even though the OS says it should be 1920x1200. It's so annoying! As Opera is usually left open I'm able to "stick it out" by quiting it or by loading another application, like Quick Time. This time VLC got stuck on my movie and I was able to captuer a video. Here's the thing - http://www.youtube.com/watch?v=5wMJenj0bng
What the **** is the problem with this thing?!?

If you select Scaled in the Display Preference, do you see 1080p...?
If so, try 1080p instead of the lower Resolution.
If that doesn't help you may need to get a > Mini DisplayPort to Dual-Link DVI Adapter to support that 27" monitor, because the HDMI port really only supports 24" monitors up to 1900x1200.
Video Support
Works with almost any display or HDTV.
Thunderbolt port with support for up to 2560-by-1600 resolution
HDMI port with support for up to 1920-by-1200 resolution
DVI output using HDMI to DVI Adapter (included)
Support for dual display and video mirroring
see > Mac mini (Mid 2011) - Technical Specifications

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Dears,
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You can try this...
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defaults delete com.apple.mail ColorQuoterColorList
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Message was edited by: J.K. ROFLing

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Try a reset ...
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Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.
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