"Some" VST Insruments are out of tune.

I did update to SE3.1.0 (I previously had v3.0.1) but it didn’t seem to make any difference. I also ran the content updater but nothing changed. The “Trumpet Combi” is from the Halion Symphonic Orchestra, and the “Small Pipe Organ” is from the SE2 Pro Set (see attached). I have to sharp the trumpet combi about +25 cents to be in tune with the organ.

I don’t think it’s a problem with just this score, but I haven’t tried creating a new one with the same instruments to see if it’s the same problem. Any ideas?