I haven't seen installing the JDK do that on any version of Windows (guessing that it *is* Windows, 'cause that's where most of the games that have FPS considerations are) but so far, the systems I've built or used are on Win7 and earlier.
What I have seen cause serious slowdown from a small change is paging, but that's usually only with trying to run newer versions of Windows on older systems with 2GB or less of RAM. You'll see the hard drive light on pretty solidly when this is happening--each task switch causes pages to be written to the swap file to make room to read in pages for the new task. This is "thrashing", and it happens when the "working set" of pages needed for all active tasks to run smoothly is larger than available memory.
In any case, some resource is being hogged (probably one of CPU, disk, network or memory) and you can find out who is doing it with the system resource monitor.
Use the start menu search (or Cortana on 10 I guess) to find it. There's also a button on task manager's Performance tab.
Also use blinkenlights on your computer. If the disk activity light is solid on, then you've got either lots of disk I/O in a high priority system task, or possibly thrashing. If not, it's most likely CPU or blocking on network I/O.
Good luck!