I turned of my mac vlc&transmission disappeared?

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So I turned off my mac to go to bed then the next day when I woke up vlc and transmission disappeared from my doc and I had to reopen it by going into my trash and finding it there and opening it up When I opened it up it said this is a windows application or whatever Anyone know why it did this?
 
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Your Mac's Specs
2012 MBP i7 2.7 GHz 15" Matte - 16 GB RAM - 120 GB Intel SSD - 500 GB DataDoubler Mac OS 10.9
Are you opening them correctly?
When you download VLC or Transmission they come inside a Disk Image (A someName.dmg)
What you need to do is copy the actual application out of that and into your applications folder and then open it from there.

Otherwise your going to have exactly what your describing, since OS X unmounts Disk Images when it reboots.
 

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