Giorgio,
I am not a fan of batch processing since you surrender lots of control over the process and your issue is a good example. It will take a bit longer, but a good solution is to use the ImageCalibration and ImageIntegration tools to create each Master Dark and Master Flat separately and in doing so then you can point to just the right Dark Master for each flat set (after you have created separate dark masters, of course).
In the event you are not sure exactly how to do that for flats and darks using ImageCalibration and ImageIntegration, here is a copy of my cribsheet which will walk you through the process. I am posting this from work (shh, don't tell anyone) so this is an older version of my cribsheet (if you want the latest version in Word format so you can tweak it to your own needs, just drop me an email) but the workflow on creating dark and flat masters with ImageCalibration and ImageIntegration has not changed so that should work for you. The information you need is on pages 3 and 4.
I hope that helps.
And, by the way, if no one has welcomed you to the forum yet, Welcome Aboard!!
Best,
Jim