Ok, finally got all of the upgrades done on my GroovyArcade install (circa 2013) to run these new binaries. For those interested, I had to upgrade or install the following:
pacman (arch's package manager) this also required removing some stuff to get the dependencies working
change SigLevel since I could not get the pacman security keys working
qt4gui
sdl_ttf
sdl2
libpng
updated romset (Centipede, etc seemed to have some files renamed), since the romset I got uses .7z I upgraded everything replacing my .zip
Dropped the new binary in and unfortunately I get no trackball at all now.

Doesn't register for non gameplay usage too, like in the tab menu for assigning keys, etc.
It does work in advmenu as it has in the past
I have trackball_device set to mouse as it was before
Anyone else having this kind of issue with these new builds? Or have any ideas on how to debug this?
~telengard