I have a partial solution, although not a correct one. I've messed with this for some time and it appears that it doesn't do this on all tables. Some tables are saving nvram files correctly.
For those that are not, hitting F3 to reset pinmame prior to exiting a table ensures that the nvram file is being re-written.
I'll continue to mess with it and see if it is only a certain class of tables with this problem, and maybe we can bug fix it better that way. For now, hitting F3 ensures I have a new nvram, and therefore, a saved high score.