Another possibility is that the students have gotten opped out of their servers somehow.
To Do on each student's account:
First, make sure your Minecraft username is set.
To make sure it's set correctly, go to the Account (gear) tab in the middle of the LearnToMod homepage. Then check that your Minecraft username matches what you see on your Minecraft launcher Exactly. It most likely shouldn't be an email. It should match the name you see next to the Play button on your launcher. (Welcome, __ )
If it IS set correctly then you can try using the command square on the server admin page to run "op YourMinecraftUsername"
You can also try typing /op YourMinecraftUsername into the chat area in minecraft when you enter your world.
Just replace YourMinecraftUsername with your real minecraft username.