I installed this mod with several others on an existing save in the latest version (0.13.10). The error message is:
Error while running the on_configuration_changed: nixie-tubes/control.lua:273: attempt to index field 'nixie_tubes' (a nil value)
Hmm...and when I start a new game I get a different error:
Error while running the event handler: nixie-tubes/control.lua:242: bad argument #1 to 'pairs' (table expected, got nil)
I added nil checks to the code at the specified locations, and everything then seemed to work fine.