Many of my equations are coming out this way.
They look perfect in the document and when saved as PDF. I am using MathFlow. Anything I can do to fix this or ?
Are they inside anchored frames?
Yes they are inside of anchored frames.
IIRC someone else had an issue with equations in FM2017 - I would make sure you are fully updated, and if it still persists, log a bug with Adobe to get it on their radar.