You must have excited those dormant skate-specific muscles too much. 90 minutes may be a bit excessive after a long hiatus. I find if I break it up half-skate - half classic in the beginning of the season, my body takes it better. But I know, skate skiing is so much fun - can't stop once you started.
My goal is to be somewhat ready for the US Ski champs in 4 weeks, and that will be pure skating. I knew that 90 minutes would be a lot, and had to remind myself to go for only that long. It proved to be a bit too much.