There is only one version of the control panel for the Lite version (it is 2.5 and I think it displays that in the output window when you start it). Unfortunately I think you found a corner case with that control panel. Without inspecting the code, I suspect the developers just disabled GUI components without gutting the internal code with the assumption that no existing services would be installed. The problem is that the control panel detects services based on names and will try to control the service if it is detected.
As a workaround, you should be able to use the Control Panel Version 3 developed for the full XAMPP version viewtopic.php?f=16&t=48932
It will give you errors about Tomcat, Mercury, and FileZilla being missing but you can ignore those and not use those buttons on the control panel. You can then adjust the service names / port detection settings in the Config > Service and Port Settings window of the control panel. This will stop it from detecting other instances running on the same computer. You will also have to have your portable XAMPP Apache/MySQL listening on a different port if you want to run the existing and portable ones simultaneously.
I have planned to add Lite Version compatibility into that version 3 control panel so it can be a proper replacement but it is just not there yet.