One or two of the rare reactions may never have been defined correctly, but otherwise the bot should be countering. Off the top of my head, three issues that I know of that cause it not to are
a) extreme lag (either network or the bot just not getting enough CPU cycles)
b) chat window issues. changing chat windows causes script triggers to re-fire, and the bot to become totally confused. make sure your "main" chat window is the active one, and don't ever change while crafting
c) incorrect settings in ReactionArts.xml. I'm not aware of any problems with the distributed file, but you can find a clean one in the SVN repository if you think you need it