Dunno if this is the right forum to post this in but, maybe it will find where it needs to go.
Followed the instructions cheeseweasel.net for setting up the secondary update to install Lawful_G d20 set. Everything went swimmingly. Created a character and as soon as you set your first class level and pick a race, it adds 2 to the reflex save. I tried it backwards and forwards with other classes and races and everytime it miscalculated the saving throws. Just to make sure, I deleted the d20 game system, reinstalled it and the Lawful_G set, and got the same results. Deleted everything again (files too!) and just installed the stock d20 system, no issues. It would seem we've got a bug in the calculations somewhere.
Running HeroLab v4.0b #315 on a Mac. Installed Lawful_G_d20 v1.7
There's a community set bug thread where this was reported. It is fixed and will be available in the 1.8 release later this month.