So I took Duct Tape and KVH's advice in the thread I linked above, which was to add a delay before each IR command in the macros and now its working perfectly. I swore I tried it before and was still having trouble but its good now so I won't question it. Now commands are sent to each specific device only which is what I wanted. Just to verify I removed the delays and the problem came back so it looks like it is some kind of bug still.