Have you selected Manual Positioning > Incorporate in Document Options > Music spacing? Have you DEselected Automatic Music Spacing in Program Options > Edit?

Hmmm, that's a new one for me.  Of course I often manually straighten the notes to the correct spacing...but that is time consuming in a large score.  Will try it with Manual Positioning.  

Thanks for the suggestion. 

Generally I only turn on Automatic Music Spacing when I'm entering notes. Afterwards, when I'm fine-tuning the score, I always turn it off. If I need to respace anything, I do it manually by selecting the music and pressing '4'. Make sure you always keep Automatic Update Layout turned ON, though! For the rest, take a look at the manual as to how Finale behaves differently with the different Manual Positioning settings (C|lear, Ignore or Incorporate).

What you have to realize (which, I guess, you've figured out now) is that "note spacing" and "Automatic Music Spacing" (AMS) clears "beat chart spacing" adjustments. So, it is a necessity to turn off AMS if you are going to use the beat chart. I follow a similar workflow to VAUGHAN SCHLEPP, though, I very rarely (if at all) use the beat chart.

Like Vaughan and George, I also leave Automatic Music Spacing on, only while I enter notes in scroll view, and enter the first set of lyrics in page view. Then, I turn it off for additional lyrics and tweaking the layout. I’ll make any other spacing adjustments on a limited basis by hand.

And, I don’t fiddle with final layout until everything is entered, and I work front to back only. That way, anything I do (probably) won’t affect anything I’ve done!