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This thread is resolved. Here is a description of the problem and solution.
Problem: When WCML is enabled, many pages on admin are using the function WCML_Multi_Currency_Orders->get_orders_currencies()
This function, is making a query that in our case takes anywhere between 2.5-4 seconds to run if there are hundreds of thousands of orders.
Solution: Installing a caching plugin will help to resolve these slow queries.