Using /spawner on a freshly placed spawner will not change the mob type regardless of the type of mob the first time you enter the command. It will however spawn one set of the correct mob type and typing the command again will properly change the spawner. There were no console errors and only just noticed the issue in Spigot 1.9.2.

Cannot confirm, am on 1.9.2 and I am not having this issue.

I am using the following steps to reproduce:

1: /give pickernickel spawner
2: Place spawner anywhere.
3: Look at spawner and type /spawner Zombie
(Command will fail to change mob type but will spawn a set of zombies.)
4: Type /spawner Zombie.
(Command will succeed and change spawner type.)

Yeah, cannot reproduce.

It seems like the issue isn't Essentials. I went back and tested all the plugins I had installed and the issue only existed in certain worlds. I will have to double check my configs but I would like to thank you for your time.