I've moved this thread to a new one because my last one has shifted topic and because I'm adding to the topic slightly. Sorry if this offends.
I have good news! I have made a device that takes IR from a replay, converts it, cleans it up and sends it to the cable box. This means one no longer has to trick the replay into hosting custom IR codes, and people with the fios problem I am experiencing can once again have a proper experience. Read on for how to do both.
As some of you know from my previous complaints, my FIOS box decides that IR input is complete a little sooner than it should. So occasionally, when the replay wants to tune to channel 123, the cable box will interpret this as channel 12, and then channel 3, and the box winds up on channel 3 ultimately. You can even see the input coming in from the replay. it is indeed a little slower between the 2 and the 3 than it is between 1 and 2! No amount of tweaking custom remote codes fixed this, and the fios STB doesn't let you "require enter" or anything nice like that. argh!
I've utilized a small microcontroller (atmel t89c5115, but almost anything will work), an IR receiver/demodulator, and a photodiode to take the IR from the replay, index it, clean it up (remove excessive space), and retransmit it. My fios IR now works perfectly! Arguably, i should replace the IR receiver/demodulator with a hardwired demodulator, which i will do when i print the circuit... Not a big deal!
It does technically slow down channel changes a tiny bit. However, you can speed up the replay's IR out to full speed now, so your channel changes may actually be FASTER! After data are received, it is very quickly sent (much more quickly than replay normally can) to the cable box.
Futureproofing the replay/No more uploading custom codes:
So lets say you have a cable box that replay simply doesn't know the code for... All you have to do is tell the replay to send out General instruments codes, and find out the bit pattern for your box, give that bit pattern to the microcontroller, telling it what 1,2,3,4, etc should be, and voila! Wrong data in, Right data out!
I'm still working on the last part, as i don't have any other boxes or remotes for data, and various boxes' data work differently, but if anyone is interested in either aspect of this fix, let me know (PM or post), i can give you the circuit diagram and my code (the FIOS fix works perfectly, the convert other boxes part needs a lot more work) and you too can have a working replay and fios!