If you look at the SEVERE log messages in the Server.0.0.log file, you will see a number of these:
Caused by: ERROR XSDF1: Exception during creation of file C:\Program Files\dynaTrace\Dynatrace 6.5\server\repository\dynaTrace65\tmp\T1489475397758.tmp for container
These might result from a read-only file system:
Could you check your DT install sub directories to make sure they are not read-only?
One thing you can try to alleviate Derby embedded DB issues is to stop the server, and backup and then empty this folder:
C:\Program Files\Dynatrace\Dynatrace 6.5\server\repository
The server should then start over with a new Derby DB on the next start.