0. Log into the server and stay in the same dimension for now.
1. Go into creative mode and give yourself a command block.
2. Place it down and try to right click it. GUI should pop up. Good.
3. Use /mwtp to go into another dimension, eg. a custom created one.
4. In that dimension, place another command block and try to right click it. You won't be able to.

Trying to switch to gamemode 0 and back to 1 doesn't seem to change anything.
Relogging makes the command block GUI work again, but switching dimensions (including going to the "default" one) results in the same issue that has to be fixed by relogging.

MC 1.12.2
Forge: 14.23.5.2811
ForgeEssentials: 12.3.56

set debug = true and provide log please

Just popping in to confirm this is an issue- I was looking for a solution thinking command blocks were broken entirely, but sure enough after logging in and testing without switching dimensions it works.

Edit: It's not specific to /mwtp dimension switching, changing dimensions by entering something like a Nether Portal etc. causes the problem as well.