Installing and unstalling VWR will not affect your software deactivation unless you deactivate your software. If you feel that there is something wrong with your agent, just unistall then install it again. Do not Deactivate the software. We use that software deactivation limit to avoid the abusing the key like using it in a lot of computers.
After uninstalling the agent, try to delete all files in the installation folder. If this will not solve the issue, then we should have a TeamViewer session for us to indentify the problem because we can replicate your issue on ourside.