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You can "repair" MicroStation in a manner similar to any other Windows application, but what you describe does not sound like MicroStation needs to be "repaired". In the first case, it sounds as though MicroStation is being started in "high security" mode, and any application that is not digitally signed during our product build process will not be loaded. There is more information regarding "high security" mode in Help > Contents.
AFA the "not activated" message... did you activate MicroStation at some point? If not, it is likely that the "30-day period" since installed (or last submitted usage logs) has surpassed. Depending on what you have (or have not) done regarding activation will determine what your next steps should be to resolve that.
Details said, Some applications were not loaded because their digital signatures could not be verified.
Now I also get the message on start up This session on Microstation has not been activated and will timeout in 15 minutes.
Is there any command that will allow the program to diagnose and repair itself if I put the installation disk in?
Any help would be appreciated.