This issue is already discussed in this thread:
https://forum.cockos.com/showthread.php?t=228101
I'm reporting it here not to get lost.
It looks like MIDI editor colors are not working properly in Reaper v6.01 when using "Default 5.0" theme.
The problem is that selected notes cannot be seen, or you might be able to see them but the colors are very very faint, in items that are set to be 'visible' and 'not editable'.
The problem is seen clearly at least in 'Velocity' coloring mode.
This is OK:
This is same after switching to "Default 5.0" theme.
The selected notes are invisible.
jnif