Hi Evereyone,
I did a lot of research and found a solution to this problem and I don't have this problem now for the last couple of months. First of all, rest assured that this is not a hardware issue. This is a problem with the vulnerable nature of Launchpad. If you have any third party app, that interacts with Launchpad or Launchpad icons or the dock, you will have this problem. For example, if you are using any app to remove or organize icons from launchpad or if you are using any app to alter the appearance of dock, you might have this problem. You see the thing is, when you start your computer, the first things that start are the launchpad and the dock. Now I have discovered that these small third party apps interfere with the normal processes of the launchpad and dock. When dock and launchpad try to start, they have a conflict with these third party apps, the result is a blinking screen, because desktop is again related to the dock and launchpad. So the desktop tries to come along with dock and lauchpad but their intiation routines get stuck with these third party apps (which are actually trying to alter the dock and launchpad at the same time), resulting in a pretty much bad functioning computer with a blinking screen and no dock, sometimes.
Now, you might think. that unistalling such apps, reinstalling the system and restoring everything from time machine will do the trick but no, this is not it. Do the follwoing to get rid of the issue.
1. Take a time machine backup.
2. Re-install the system. Do not restore from time machine but reinstall a clean system from internet.
3. Again, do not restore your data from time machine, instead re-install all the apps you need from scratch and avoid re-installing any third party app that interact with the dock, desktop or launchpad.
4. Restore your data/documents but not "settings" and "other files" from time machine using "migration assistant" in utlilitiies.
5. Your brand new system is ready. It might take some time but you will get a fresh system without any problem.