The 2.6+ installers check the version of Eclipse they’re being installed on to ensure that 2.6.x is installed on either Eclipse 2.1.0 or 2.1.1 and 3.6.x is installed on Eclipse 3.0M2. It does this by verifying that the .eclipseproduct file exists in the Eclipse directory specified and by checking the version of one of the key Eclipse plugin directories. Which one in particular escapes me at the moment.
As Michael correctly pointed out, we base our testing on the Linux packaging provided by the Eclipse organization directly, not any third-party suppliers. Another alternative for you is to use the Eclipse Install / Update perspective to update to the latest version from our update site.
–Scott
MyEclipse Support