I had this happening on my old machine the last 3 years or so, when you start the client it has super low FPS … waiting a couple of minutes and it suddenly goes to normal for the rest of the session. Nothing you can do about, no setting no activity. It was a major issue for me when disconnected while in fleet/combat. Also it forced me to stay in a citadel overnight or I wouldn’t be able to safe undock after login.
It’s not happening with my new rig, at least I do not notice, as the machine in 10x faster.
Internet connection problems can really choke FPS in EVE. You won’t get disconnect unless you start drooping packets. But it gets all wonky when client tries to load stuff and your connection can’t keep up or when you get desynchronization issues because ping exceeds 1s. Good old times playing using 2G connection, with my phone as router…
Did you clean out the heatsink? Max temp for the Xeon e5440 is 67 degrees. So, it probably was thermal throttling. Moreover, excessive temperatures can cause damage to CPU. Thus, I strongly suggest blowing out all the dust in your computer with compressed air, making sure all the fans are working, ensuring the computer has good air flow (i.e. nothing is blocking intake vents), and replacing the CPU thermal paste if needed (do a youtube search for tutorials).