Now, I could easily be wrong here, but this comes up occasionally... And I recall reading that what your seeing is more of a quirk of how things work in windows than anything else. When you bring up the Task Manager, CoH is no longer the primary focus, so fewer processing cycles are dedicated towards it.
I'm fairly sure this is what's going on, but you may want to wait for more tech minded individuals than myself to either confirm or refute my answer.
"My inner mind has become a reality-cracking overgod. He torments me! Help!"
TGH got it. When you look at taskmanager, CHV no longer has focus. You'll have to seek elsewhere for the cause of your performance woes.
I'd start with the following:
Upgrade all drivers
Defrag all drives
Verify all items in the registry currentversion/run keys that are starting at startup should be. Kill those that shouldn't be.
Same goes for items it startup directories for local user and all users
Sweep for spyware
Be well, people of CoH.
Turn off AVG or Avast virus scanners while in CoH, or figure a way to disable the constant shielding. I never had a problem with AVG, but when I was researching what was wrong with mine recently, in addition to Avast, AVG can cause issues.
Avast's problem might be it's conflict w Windows Defender. When two programs are trying to find spyware at the same time they butt into each other, or something.
It took a while to get CoH back to normal after I reinstalled Win7 due to a hard drive failure [I did have a backup, but it sucked and didn't really contain what I valued most.]
If you bring up the task manager, add base priority to the displayed columns and check off "Always On Top" in the options, you will see that when you go back to the game, the priority goes back to normal. Click back onto the Task Manager, you'll see it drop again.
It's entirely normal.
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Much thanks everyone, I guess it didn't occur to me it could be the task managers fault.
Observer effect. The act of observation effects the thing you are trying to observe.
Especially true in computers since running another program, or even changing the existing program to measure itself, creates additional CPU and memory load. Danged if you look, danged if you don't. 
It also doesn't help that most other programs don't do the same priority switching that CoH does. That's just how it's programmed.
As of late I have noticed a decline in the operating of City of Heroes on my system. Anyway in task manager it keeps saying the priority is set to below normal, and every time I try to change it to something other than that it just goes back to below normal.