I found the answer to this questions after searching the forum for a little bit but I thought I'd just help anyone else out who's having this problem by posting the answer in the first post for ease of use.
When your click or download count automatically stops showing on your website and you haven't changed anything all you have to do is open your clicks.txt file and delete any extra spaces between lines. (To clarify, there should be no double spaces between the list of files.) Mine happened to be at the end of my list of files inside the click.txt file. How did I know it was at the end you ask? Because when I click at the end of the list of files the cursor was two lines down so that lets me know there was extra space at the end. I don't know how it happened though! Also make sure there is no space at the beginning of the list of files either.
Clicks/Downloads counter suddenly disappeared
Correct. I'm, not sure yet why exactly these empty lines occur, but will try to do something to eliminate them automatically in the next version.
Klemen, creator of HESK and PHPJunkyardWas this helpful? You can buy me a drink here 
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Help desk software | Cloud help desk | Guestbook | Link manager | Click counter | more PHP Scripts ...
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Help desk software | Cloud help desk | Guestbook | Link manager | Click counter | more PHP Scripts ...
Also browse for php hosting companies, read php books, find php resources and use webmaster tools