I have the following:

So I want
99% and above = Green
When you pick "percentage", this takes the values as a percentage of all the values. Since you're formatting based on the value itself, and not the value as a percentage of all the other values, you need to use 'Number' for the type and use 0.99 for the upper bound and 0.95 for the lower bound.
EDIT: It looks like the behaviour is different in Excel 2016 and one needs to actually put 99 and 95 (and not 0.99 and 0.95) as values. I guess Microsoft received some complaints or something and decided to change it.