Hello fello chess engine enthousiasts

I need your help!

I am trying to setup, since a few weeks already, a server so it can play by itself in the Computer Pool like many of you are doing.
But I have a hard time getting the engines finishing the games!

At some point in any game, the engine (either Stockfish or Komodo) just stop pondering and let the time fly, resulting in many losses. Is there something special that I need to setup in Arena to prevent this?  And how to I get my engine to remain in the computer pool without me always have to do /computer in the console?

What is your setup and configuration so things run smoothly?

I am running Arena 3.0 (since I have read a thread on Arena 3.5 breaking the ponder and making engine stops - I though I had fixed this with 3.0, but the problem is still there) on Windows 2012 R2 (or Windows 8.1), have the Syzygy tables (up to 6-men) installed and working, and a decent opening books.

Thank you very much!
-Coco2