It sounds like you have got the issue kinda resolved but I'm not sure about the current situation. Are you getting the errors with the files you need for the checkout? If so do you have the same charge rules active? If you know for sure that this problem only occurs when running multiple transactions it may be an issue related to the clearing of the session. If this is the case then having some extra code to kill off the session when the transaction completes may help. You can do a session unset like this:
Please post back and let us know the current condition with your files you are now using.