It's not a bug, it's a feature! 
Go into Engines --> Manage --> UCI (tab).
At the bottom you'll see a check box for "Common max CPU cores setting". If this box is checked, all engines will use the number of cores that this setting is set to, and you won't see a threads option when you go into Engines --> Engine 1 --> Configure.
However, if you uncheck the "Common max CPU cores setting" box, you WILL see the threads option when you go into Engines --> Engine 1 --> Configure.
Aha. Many thanks, comrade.
Also, will any of the output be different after I pause an engine and restart it other than the nps?
Arena 3.5 help says: 'Note that most engines report wrong nps counts after [pausing and restarting an engine].
Technically, all threads of that particular engine are suspended by Arena. The engine does not know about that, so it cannot adjust node counts etc. So engine info might be inaccurate after doing that.'
The node count doesn't really bother me, but what I am concerned about is the evaluation of the position or the 'best move' being wrong.
I don't pay much attention to the node count, so I can't say that I've noticed that effect with pausing engines. About your other concerns with pausing, the only thing I've noticed is that the engine will usually start the search over after pausing, unless it has some kind of persistent hash feature. (Most don't.)
It looks like stockfish 5 can handle the pause?
It looks like stockfish 5 can handle the pause?
Yeah, apparently so.
Now I have a confession to make...I have to claim stupidity. 
All this time I've simply been turning the Analyze button on and off and just assuming that that's how you pause the engine. Now that I've found the pause function (thanks to your help), I guess I should start using it. 
Is anyone else aware of any issues with pausing Arena 3.5? It seems like a very useful tool and I would like to use it a lot, but not if it means my evaluation will be all messed up.
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That's incredible! Arena chess 3.5.1 is much better than Chessbase Fritz 17, especially for engines vs engines tournaments. You can freely upgrade / remove / change every engine and parameter without losing all previous data. And freeware Stockfish and derivates are much stronger than all engines sold by Chessbase. Few open source developers agaist a 30 years old giant manifacturer that never innovates (Fat Fritz is copied and hosted by LC0)
Hello new chess friends!
Just started with 3.5.1 today. I want to use all my PC hardware to play Engine vs Engine!
Dual Xeon E5-2687W V4 Cpu's 12 cores each so 24 cores or 48 threads.
256GB memory.
Much thanks!!!
I can't adjust my threads from 1 to 2. In Arena 3 I could by going Engines>engine 1>configure and there would be an option that said threads and i could adjust it there, but 3.5 doesn't have that option. What do I do so it uses 2 threads?