Corrupt file type icons in finder

Hi there,
I discovered a problem with small icons in Finder and it's driving me insane that I can't figure out how it happened and how to remedy it. Hope anyone here can help!
The symptoms:
The problem concerns .mkv and .srt files. In the list or column view in Finder, these file types have exec icons instead of the regular VLC icons. However, when I change to icon or cover flow view, the correct VLC icons are shown. Also in quick look the correct icons are shown. So, the problem only seems to concern small icons, but not large ones.
I tried to change the icon via Command+I. The preview icons are correct, only in the tool bar the incorrect small exec is shown. However, when I drag-drop the small exec icon from the bar to the large item, also small exec icon in Finder changes to the correct VLC icons. But only for this particular file and for all files of that type. Also when I download a new .srt or .mkv file the small icons are again exec images. SOO weird!
What scares me a little is that I did a another clean install of Yosemite after I discovered this. And nothing changed! What is happening here? I hope someone can help!
Potential cause:
The problem wasn't there after I updated to Yosemite. I did a clean install and everything was fine. However, at one point I ran the OS X version of Gmaptool (a .img merge app for Garmin navigation maps). The app is only a command line and the file also has an exec icon. After I ran this command line, the problem occurred. Does anyone know how this could have happened?
Thanks for your help! It's driving me insane!

Perhaps it's a good idea to upload a few screenshots
As you can see in the first three pictures, only small icons show the exec icon. Large ones are the correct VLC icons. The last two show the Info windows. In the first one, you can see the small exec icon in the tool bar. It changed after I dropped this exec icon on the icon field (see second Info picture). However, this only changed the small icon for this particular file, not for all .srt files.
Is there some weird preference causing this? I also found a few system files now have exec icon (see picture below). I think that wasn't the case before. How can I change it? Can I reset the small icons somehow? Would it help to securely erase the hard drive? I have nothing on the drive anyways, so that would be an easy option for me.
Thanks!

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