There are a few issues that effect this.
1) Lowering graphics on a high end PC and actually negatively impact fps performance on minecraft
2) Using graphics accelerators improperly can be a huge impact; I.E. shaders, mods, texturepacks
3) Certain mod blocks can effect fps
You can try:
1) Test to see if issue is isolated in areas around machines or blocks
2) Changing minecraft vanilla graphics settings; vsync. render distance, graphics level, etc
3) Change computer graphics settings for minecraft, most default settings arn't tailored towards Java
4) Remove all texturepacks/mods that change graphics
Very last thing to do would be reinstalling modpack > clean reinstall of Java > clean reinstall of drivers
