OK, I’ve just checked, there’s been no changes to sh2peaks beyond those required as part of the update - it should behave identically. Moreover, we’d have picked up any difference in the automated testing. So I think the issue is something else.
As @rsmith says, the warnings you see are issued when the code encounters header entries it doesn’t know about, just to say it’s ignoring them. It should have no bearing whatsoever on the process of reading the data.
What I’d be worried about though is that you say that with your previous installation, sh2peak identified 30 peaks from each FOD…? That sounds just plain wrong… Any chance you could post the commands that led to the production of that file, and the subsequent sh2peaks command? Could it have something to do with changes we made recently to the default lmax value in dwi2fod…?
In any case, we might consider changing the way these unknown keys are handled in the Matlab code, possibly by adding them as fields in the output structure, which would make it possible to actually make use of the data, and avoid all these unnecessary warnings. Might be worth filing an issue for that…