From the GENS site:

The major change in Gens 2.00 is 32X support, i did the entire 32X support in 2 months so it's still far from perfect. I would like to thank Michel Gerrie (author of Xega) for the great 32X infos :)

Go to http://gens.consolemul.com if you wish to download Gens 2.00, and, yes, the 32X support does include Knuckles Chaotix:



Source: http://gens.consolemul.com and StH Area51 Message Board