For me it looks more like user account/data corruption or some sort of bug manifesting itself by possibly unexpected combination of different settings/preferences.
Testing with new user account might reveal this issue better and easier than any other of described options - and it is least destructive of them as well.
Option 3 should be used only as last resort and takes more time and work than any of other options.
So as you suggested I created a new user account and logged in using that, and so most of the issues I am facing with the original user id I did not face it the new user account. So what does that mean ? and what do I need to do now ?