I have seen a lot of posts about bugs in 3.6 and 3.6.1. I am hesitant to upgrade. IS it better to stay with a stable version for now while these get worked out?

3.6.1 works for many but not all. If you do a manual upgrade so that you have both your current atahualpa folder and a atahualpa361 folder as well you can just switch back to your current version if there are problems. Take a look at the new versions and updating forum for instructions on doing a manual upgrade. I would suggest against doing the auto upgrade for just that reason. If you are not sure how the manual upgrade process works I would stay where you are right now if everything is working for you.