Instant JChem uses its own Java (that it is bundled in the installer). If you want to use another Java, see How to change IJC’s Java.

Vista users who updates from 2.3.1 to 2.4: After installation of new IJC, starting of new IJC application may try to run still the old version. That is the side effect of Virtual File System of Vista. Vista protects the writting of the Program Files folder from normal users. Unless you access it in administrator mode , those files that are copied into “Program Files”, will not be stored there. Instead of that, they are saved in your home directory. Despite of it, your application can see these files in the “Program Files” folder. By upgrade, the situation is similar. If installers are run in administrator mode but update modules launched from IJC application (in non-administrator mode), two different users writes the same folder. If you would like to remove this IJC version, installer can removes only those files that arelocated into the directory that it created.
The workaround : Delete the following directory:

    
where <HOME> is your home directory and <INSTANTJCHEMPATH> is the relative path of the codebase. For example: