Thanks for the pointer. It doesn't look like its memory issue it was using:
Max heap size available: 3539 MB

Under normal circumstance. it looks like a case of not being built to handle this much load. A quick restart makes it faster again. I might use a script for now to restart it every few hours. Thanks for all the help.

Also for whatever reason the bash script is not working for me, will it be possible to call Ubooquity to use more memory from commandline? java -jar Ubooquity.jar -webadmin -Xmx (or something similar?)

Thanks I will try it as I have plenty of ram and cpu cycle laying around. Just out of curiousity, whats the default memory assigned to Ubooquity?