Yes, it looks like you are using the newest PioViewer with the older version of the solver. Here is what to do:
1)Run the updater to make sure all the files are up to date
2)In the viewer look at the bottom where it says: "connected to..."
3)If the version is different than 1.10.19 go to Solver->Connect and choose PioSOLVER-pro (or edge/basic depending on the version).
It should happen automatically but sometimes the updating process gets interrupted or something else unexpected happens and it doesn't. Once you are connected to the newest solver it should work without problems.
Test it quickly without solving (just build a tree and try to save it) so you don't waste any more time.
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If I have multiple trees calculating at the same time, what determies how much CPU resources are dedicated to each tree? Is it the order in which the trees began running, the size of the trees, etc?
If you are running a script then they are solved one by one. If you are running multiple instances of the solver then build in operating system scheduler decides and there is nothing solver instances can do about it (they don't even know the other one is running at the same time).
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Is there a way to force PIO to focus on certain trees and dedicate more CPU resources to those trees?
There is nothing you can do about it. The instances are independent with the exception of PioViewer settings file although you can make them fully indepdendent by copying Pio instalation folder and running every instance from another location. You can try reducing number of threads some of the instances are allowed to use (Tools->Configuration->Behavior) but be careful with it if you start all your Pio instances from the same folder as they use the same settings file.
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Is there a limit (besides RAM) to the number of instances of PIO I can have open at one time, or the number of trees I can simultaneously calculate.
Nothing we are aware of.
The EV is calculated against current strategy of the opponent which is not perfect equilibrium yet. That's why there might situations where EV at a given time is slightly negative for a chosen action. The better accuracy you reach the smaller those disrepances are going to be.