Ever since I wrote this post, I’ve paid more attention to people’s reactions to my けっこうs and my いいs. To be honest, I started using more いいs than けっこうs and have noticed far less confusion on the part of the employees. I was generally using 「けっこうです」 or 「袋はけっこうです」- the most common situation where I have to refuse something – and often noticed that the person would respond with 「いいですか」I wrote that けっこう might be easier to understand from a non-native speaker, but I’ve started to think that might not be the case.
I’m using the same phrases just with いい. I’ll have to start mixing it up a little more to see the results. I’m still convinced it could be my intonation with けっこう – there are more syllables to mess up.