Sounds to me like your seat height is roughly what it should be, too.

But IMO those adjustments need to be made GRADUALLY if you weren't having major problems with it before (hips rocking, having to point your toes, pain behind your knees, etc.). Your muscles need time to adapt. If it was me, I'd take the seat height about 3 mm below where it was, ride it for a while, then lower it another 3 mm, and repeat as needed until it was where the LBS thought it should be. But be advised that a free "fitting" is just a rough guesstimate - a "real" fitting involves taking all kinds of measurements and watching you on the bike for quite a while - and even a skilled fitting involves a lot of judgment calls.

So it's definitely possible that where the LBS set your seat height isn't exactly right for you. But if your leg was straight at the bottom of the pedal stroke before, then it was definitely too high. Hips rocking is a big red flag too (you're moving your hips to try to reach the pedals, basically), but there are other things besides seat height that can cause that if you have misalignments in the knees or hip joints.

If you were having knee pain with the lower seat, I'd take that as a warning that maybe it was too low. But if it was muscle pain or cramps as it sounds like, lower it gradually and see how you do.