First, make sure you have set up heatmaps properly as detailed in the heatmap guide
If you have set them up and waited at least an hour for the changes to take effect, the cause may be one of the following:
Cookies disabled via clicky_custom.cookies_disable
To log heatmaps efficiently, we store click data in a cookie that is then relayed to us once every 5 seconds. If you have disabled cookies, heatmaps will not work.
Does your site user the Prototype
Not enough visitors
We only log heatmap data for a random 50% of your visitors by default, although you can increase this on the upgrade page
with the custom plan option. (We also don't log mobile visitor heatmaps [yet] because we haven't had a chance to test them thoroughly).
So if your site is low traffic, there is a reasonable chance on any given day that you won't have any heatmap data logged, as maybe you only had 10 visitors, and only a few had more than a single page view, and those few happened to either be mobile visitors, or not
randomly selected in the 50% pool.
Pro Plus or higher account
Heatmaps require a Pro Plus account or higher. The option to set them up still appears with any account level, but they won't work unless your account has access to heatmaps. If desired, you can upgrade your account
XHTML interferes with the encoding as we pass heatmap data to cookies and get it back out to send to our servers. We're not sure why this occurs and we spent many many hours trying to hack around it, but were unable to find a fix.
Extremely long web pages
Webkit based browsers (everything but Firefox and MSIE) won't draw canvas elements taller than 10,000 or so pixels. So for very tall pages, if you're using one of these browsers, likely you won't be able to view a heatmap for it. We use canvas elements to draw the heatmaps dynamically on your page at the time you request them.