
Only having 2 pups in the second litter may have meant they were bigger and therefore harder to whelp, if there are more this time then hopefully she will have them normally.
I would keep a close eye as there are other reasons for c/sections and the uterus may be weaker from the previous section and rupture if things don't progress normally,hopefully enough time has elapsed between the last litter and this one for her to have fully healed inside.