It is quite possible to have several versions of Bocop on the same machine, for instance if you want to upgrade while keeping your previous version just in case.
In this case, however, you have to make sure the Qt interface knows which package/version to use when building the executables for your problems.
This is done in the menu bar with the ‘Set path’ option, in which you simply have to give the location of the root folder for the Bocop package (meaning the folder with the README, INSTALL, LICENSE, etc files).
The GUI already checks by itself that its version number matches the version number for the core package, but this check will fail for instance if you use both a precompiled and source package with the same version number.
So in short, when you install a new package on a machine with a previous install of Bocop, please make sure that the path to the root of the package is correctly set. Menu bar -> Set root path.