I gave this answer last night aswell to a simulair question, maybe put it in some keyclone howto ? If it fixes the problem ofc, wich it did for me on several macro's en setup's already. And it might ofc be a Keclone bug, so it will be fixed anyway.

For now, do this:

If you want to use 6 and alt 6 ofor different WoW's, make sure that in the WoW client where you do NOT want to use the alt-6, you bind alt-6 to NO button / action. So, when it's pressed, it does nothing.

This way you can use 6 for action one and alt 6 for action 2, and ofc just use RR if you like.

Can't really write it down in a better way, hope you get the point