I accidentally typed in the command /debug into the console and this popped up.
[00:54:19 INFO]: Vanilla debug profiling is disabled.
[00:54:19 INFO]: To enable, restart the server with `-DenableDebugMethodProfiler=true' before `-jar'.
[00:54:19 INFO]: Use `/timings' for plugin timings.
Have I disabled Vanilla profiling or something?
No, that means that if you want to use /debug you must add the specified command line as stated in your logs.