I was hoping that was it. Unfortunately I don’t have access to any of the other modules that may have caused this, so I’m quickly running out of ideas.
Next step that I would suggest. Setup a fresh magento environment that has the ability to switch currency.
Test to make sure that you can go change currency after adding an item to cart.
Then one by one the modules that you have. After each module gets installed and enabled, make sure you can change currency with an item in the cart.
If it errors out after you install a module, then you have your problem module and then it will be easier to narrow down the error.
Alternatively, you can check ALL of the config.xml files and comment out ALL events. Test the cart currency change and begin to uncomment out the event blocks for each module if it started to work.
If none of this fixes the situation, then its going to be server related (but I doubt that).
If the timeout only occurred on the cart page, it could be code in the theme template, but it sounds like its every page once its times out, which would be code related.