Without seeing some logs it will be hard to tell you what is going on have you opened a case with support?
If u have SAM, then try to check the details on all Solarwinds processes and if its reporting any issues on it...
Curious if you're running antivirus software on your Orion server. I've seen AV do weird things like you mentioned above. If you are, what are you running?
This is a generic AV file exclusion list for Orion.
Perhaps see if you have disable AV for a day and see if the performance issues go away.