The issue comes from the way WooCommerce handles rounding and provides the data within the code.
We are working hard to get this done, and I've just recently assigned somebody to focus on this plugin full time, so we'll be able to get a lot more updates done more quickly.
In the mean-time, if you can get by with flat-rate discounts those shouldn't cause any problems. I'm assuming you're working with percentage based discounts now..??
Do you have logging enabled? If you can send me the log file so I can review the request that generated the error that would help.