You might want to try running the Modeler or Service Console as administrator. I'm not sure, but the error message seems to resemble one that could occur with previous versions versions of the modeler, see https://forum.mendix.com/questions/1522/An%20error%20occurred%20while%20reading%20the%20Application%20Model%20%28run%20as%20administrator%20issue%29
Are you sure this is because of the profiler app? It looks like it's a db config issue: "java.sql.SQLException: unable to open database file at org.sqlite.DB.execute(DB.java:275)"
What happens when you remove the profiler app from your model?
What kind of database are you trying to use on the server?
I would highly suggest not to use the build-in database, not even as a test because it just is not representative enough. It works nicely during development and for unit testing but after you have a complete version of your application you should move to a more mature database.