Before you try the steps below, check that you aren't in punch record mode.
I had the exact same problem.
I think there are many answers in this thread that don't understand the problem.
You don't need piano rolls or the like if you have a midi controller.
I have 3 instances of the same soft synth running different patches.
If you look at track 15 on the bottom below, you will see that there are no dots in the lane to the right of the clip.
For some reason that seems to indicate something but I think it is co-incidental.
The virtual controller I am using is a Nektar LX25+
I went through all my tracks that were using midi input and reset the input on the inactive tracks to none as shown below then it worked as normal.
The small clip in the lane was recorded from the keyboard.
I hope that helps.