Coollector doesn't decide on its own to use one video player or another. Coollector just launches the video player which is associated with the file extension.
Here's what probably happened (I use random file extensions): you launched an avi file and it was played by VLC because the .avi extension is associated with VLC on your computer. Then you launched an mkv file and was surprised that it's played by Mediaplayer but it's because the .mkv extension is associated with Mediaplayer on your computer.
To fix your problem, you must find which extensions are not correctly associated with VLC. Then you use Windows Explorer to locate one such file, you right-click the file, you select "open with", then "choose another app", and there you choose VLC and click the checkbox "always use this app".
Now VLC is associated with this file extension