Are you running EPiServer CMS 5?
To compare two versions in EPiServer CMS 5 edit mode, make sure you do do like this:
First you select one version to view by clicking the "Select" button in the version list. This will be the version displayed in the left hand side of the comparison. Then you select the version to compare with by clicking the "Compare" button in the version list. This will be the version displayed on the right hand side of the comparison.
When you do like this, is it still not working?