First of all - check if it counts 'shows'. If not - make sure you have rot_in.php in your templates.

If there are 'shows' but no clicks - check that you have 'rotation parameter' in your links ( like 12x34x5678).

If you have it - check rewrites. There are could be some problems with custom rewrites. Easiest way to check it: clicks on any link and save response headers. There should be Set-Cookie field in response.

For version 50+:

• You can adjust traffic count in rotation - settings and switch off count for noref\nocookie while having only this type of traffic (just starting site for example)
• you can also not count clicks from proxies and have a problem with Nginx when it counts all traffic as proxy.
• If you use rot_in.php do not add 'http://www' to src=… because it sets a cookie to www.your.domain.com, while you links may look like just domain.com/… ie without www. This prevents browser from sending a cookie