At one point you said that this continuous flashing doesn't happen with every push.
That's not what was happening on the other processor (s383) so I'm thinking that perhaps you've started triggering the low-voltage reset. On some remotes, when the batteries get low, the continuous flashing can occur. When you are doing a lot of uploading it really eats up the batteries.it SEEMS to work on my remote, in that when I press a couple of number buttons it emits a signal that works on my STB. However, it's only a matter of time before my remote "freezes" (with the IR signal being constantly emitted, like the button is stuck but the physical button is most definitiely not stuck). First time it happened with number 1. Without doing anything in IR, I just removed batteries and tried it again. Num 1 worked fine, num 2, 3, 4, 5 OK... then the same "freeze" happened on 6. Bottom line, something is not stable or right with my implementation.
If replacing your batteries doesn't fix your problem, we'll look at the protocol, but if this isn't happening with every key push, its probably not the protocol.