Make sure that you dont accidentally have two copies of Miranda running at the same time. I've experienced something similar to this when i had an old version open, and was configuring a new version to be identical (trying to get a fresh start for debugging purposes) sometimes the UI would glitch out and not accept input on one of them after a few minutes. Ive experienced the bug about 3 times now over the years, im not certain if its the -exact- cause, but it only -seems- to happen when ive got two copies of Miranda running at the same time. Sometimes just closing and re-opening one of the mirandas will fix the issue, sometimes not.
And if you didnt have two copies open, then im pretty much out of guesses. Ive been unable to duplicate the issue easily in order to report it as a bug.