I finally seem to have this sorted.
The 2 largest issues were MyTown plugin and chunkloaders.
With MyTown installed the TPS instantly dropped to 10. I also found with chunkloaders, if set to only run when the player is logged in had negative effects. Which doesn't make sense at all.
I found the issue with chunkloaders because my test server had chunkloaders on by default. When I removed MyTown from the live server, TPS rose to around 15-16 where the test server ran at a steady 19. Changing chunkloaders on the live server to always run got the server to a steady 18.5-19.5.
Ram usage is way up, using 5GB off the bat where before it was only about 2GB.
We also found that Prism gave a fair bit of block lag (No surprise with the massive amount it needs to log) I changed to LogBlock, which gives a very slight delay in blockbreak but its very bearable.
Strange stuff indeed
