Do you use a cleaning tool? Some of these tools can cause damage so that is a possible cause though I don't know it causes this situation. So if you use a tool like that please mention it.
On the other hand, browsers for example, can get clogged with too many cookies etc so CCleaner is an excellent tool which is very safe to use. I recommend running the first two pieces of CCleaner to free up space and to clean the registry and see if that helps. I don't know if it will help with your Messenger or not but it won't hurt. Find CCleaner in our
Freeware DB
I would try uninstalling Messenger using Revo Uninstaller (also in the freeware DB), then run ccleaner (specifically registry cleaning), reboot, then reinstall.