The website will show you how many executions have been 'downloaded' to the user rather than how many they have used.  To determine that, you would have to set the security level such that the installation accesses the web site on every protection check.  Alternatively, you could make your application use the CopyMinder API to get the execution count.

You can see how many executions have been 'downloaded' to the installation by clicking on 'Modify Settings for a Product Key' from your main CopyMinder Developer's web page.