Use the Score Manager to set values for different layers via a pull-down arrow in the instrument row.

Thanks, but my issue is why the flute plays in layer 2 doesn't play on eight measures of the song. It does play on all the other measures.

Forgive my confusion, but why would you want to put a flute and a sax on the same staff unless the same player plays both? Given that you say the flute plays all but eight measures, that doesn't sound like it is the case.

Yes, the same player will play both.  Using the Change Instrument in Utilities appears to turn off the flute in layer 2. The flute did play until I changed from alto to flute. 

Can you post an image of your Score Manager with the staff holding the Flute and Sax completely expanded via the arrow in the Name Column?

"Yes, the same player will play both."

Sorry but why do you need to switch layers at all? This musician can only play one or the other at a time.

If one uses the Utilities > Change Instrument routine, this is what one's Score Manager should look like. Since one player cannot presumably play Flute and Sax simultaneously, separate levels should not be required in Finale's preferred solution.

That looks normal to me. I'm not familiar with JABB specifically but use several other Garritan libraries. I'm wondering if there is something odd with the way the controls on Ch. 9 in the Aria player are configured? 

Thanks for all your help. Works now!