It seems you have problems with mods on a forge server.
Statements like “something works, but this doesnt” do not give enough information for us to help you. We need logs to se what was done, and what failed, and what error messages was produced. There are two main, and one forge log that are interessting:
The minecraft log:
/var/games/minecraft/severs/[your server name without brackets]/logs/latest.log
The forge log:
/var/games/minecraft/severs/[your server name without brackets]/logs/fml-server-latest.log
Have you tried updating woth the WebUI and the java installation?