I've had the 659 for almost 3 years, and have noticed some quirks like this. I have to go around the block, figuratively, to avoid these issues. One idea is to just always turn on the tv the same way by always using one macro, then hitting the other macro once everything is up and running. You hit the "PS3" button, let things get up and running, and then hit "watch tv" or "listen to music". This way you aren't asking the tv to change inputs while its turning on. I'm not sure there is a way to adjust for a delay. Harmony should be aware of this, but I've never seen that adjustment in their software.
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