I will confirm the bug when doing it manually (m. 1.)  However, using the plugin TG Tools > Cross Staff..., it worked fine (m. 2.) Much faster, as well!

If you are doing it manually, you missed a step. After you cross-staff using the Note Mover Tool, the next step is to use the 'Reverse Stem Tool' found in the 'Special Tools' palette. Making adjustments to the beam angle should be last (in most cases, you don't even need to).

There's also a keyboard shortcut that does all of the necessary steps for you:

https://www.finalemusic.com/blog/finale-quicktips-cross-staff-beaming/

George, 

The problem isn’t using (or not) the stem reversal tool. Even after using it, as I did, the chords were not aligned correctly, and the stem did not extend all the way to the high notes. Take a closer look at our examples.

There's actually a lot involved in the keyboard shortcut, and it always does it right. Depending on which staff the notes originate, and the stem direction, the shortcut uses the:

• Note Mover Tool
• Reverse Stem Tool
• Notehead* Position Tool
• and hides rests

Doing it manually, you can get by without using the Notehead* Position Tool by instead using the Beam Angle Tool and adjusting the beam up/down. You may need to experiment with the Reverse Stem Tool to see which how the stems are affected. With intervals of seconds, it seems best to have the notes originate from the top staff. I work with keyboard music a lot and used to do this often back in Finale 2004.

Hey George, I will give it a try Option Up arrow or Down arrow.

George,

I selected the entire set of measures, then did OPT UP, which used a staff above the piano part in the score, and then OPT DOWN and I'm happy to say it is all fixed!  It is great that it works on older passages that were messed up too. Thank you for the hint.

George, I'm finding this workflow a little tough when every other note/chord is cross staff. It is challenging to select a single 16th note chord in order to use OPT DOWN (or UP)

Any suggestions when the hands are alternating every 16th note?

In that case, you might want to give the TG Tools plugin a try. As long as you can define a split point, it should work just fine. And based on the examples you’ve posted, I don’t see any problem.

Yes, what Mike R. said. If there is a clear split point then using the TG Tools plug-in is easiest for doing a lot of measures. However, It looks like both staves are in treble clef and quite a bit of notes cross, so there isn't a clear split-point. Definitely not an ideal situation you have here. I generally don't have issues with selecting 1/16 subdivisions. You could try widening the measure width temporarily to give yourself room, but make sure to turn Automatic Music Spacing off so things don't get respaced in the middle of making an edit.