To me it sounds like too much flour added during the roll out.
If the first one worked then your mix is probably fine, perhaps borderline on the dry side, but when the subsequent ones (which had re-rolled dough fragments added in) were flaky/rough, then your mix is possibly drying out too much so that the dough can't be melded again properly after it has been rolled out with the flour added in during rolling. Microwaving the dough would only worsen this I suspect.
When I make my gingerbread dough, if it calls for 8 cups flour, I put in 7.5, then freeze the dough, and later when I'm rolling it out I know I've got wiggle room to add the remaining flour in during the kneading and rolling phase without drying out the dough.
If you still have dough left and want to try an experiment, I have "thinned" my dough out with milk in years past, add a little dribble at a time and knead it into the dough to moisten it a little, this should help combat the drying out
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