It shouldn't force you to switch every time. At least it doesn't for me. Send a bug report to fizzer.
Chrome forces you to approve flash each time you use it. That is what OP is talking about.
But every time in a game when I get to the stage of deploying troops in any turn, the game freezes, and then my screen goes black and I basically have to restart my computer. Any ideas as to what might be causing this issue?
Haven't heard about this before. Might be time for a bug report.