Can you please zip up and attach here a minimal case that reproduces the problem? Evan, in your case, hopefully exporting just one flow from one of your monster projects would be sufficient for me to reproduce the problem.
We have just today fixed a bug with the way that lyrics are automatically adjusted to try to avoid changing the rhythmic spacing. We have not yet established whether this bug fix will be safe enough to make it into the forthcoming minor update; it has the potential to change the appearance of lyrics in existing projects so we need to take some time to look at a lot of projects that use lyrics to see what the effect is.