If you've never had them before it may be part of the cleansing process...cleaning house everywhere! Clots can also occur with uterine fibroids and endo...but in those cases you probably would have had problems for some time.
It's interesting because in Chinese medicine the liver is involved with flowing and spreading. When funcitoning properly it adjusts and smooths the movement of Qi and blood. When out of balance it can cause Stagnant Qi or Congealed Blood...and one of the symptoms is passing clots during menstruation. Perhaps your flush got a lot more moving than just Gallstones and parasites!!!