Hi Erik,
There was a bug for a few months where Skyline was always reporting the number of concurrent precursors even when the y-axis was labeled as reporting concurrent transitions. Perhaps you have one of the Skyline versions with this bug? Do you have a consistent number of transitions per precursor (e.g. 3 - 6) where you could simply do the multiplication in your head and confirm that the counts differ by that factor?
Hopefully, if you updated to the latest version of Skyline-daily (22.1.9.208) or Skyline (21.2.0.568) you would see this problem fixed in those versions.
Otherwise, can you please provide screenshots of what you are seeing and upload your Skyline document (use File > Share to produce a .sky.zip file) to the following link?
https://skyline.ms/files.url
Thanks for reporting what you are seeing.
--Brendan