Input codes fall under General IR Codes, so your setting of 4 will repeat it 4 times. (remember, this repeating is only to help ensure the message gets delivered - it doesn't try to actually change the input 4 times) Basically you want your repeats to be as high as possible without the receiving device actually thinking it received more than one command. This may be as low as 1, or as high as 5 or 6. It depends on how often your device actually looks for IR data. If you press the number 5 on your remote, and you are getting a repeated effect at your TV (it tunes to 55, or 555 etc), then the general repeats need lowered. Lower them one at a time until the TV (or other device) responds by just tuning to 5.
The exception for me has been volume IR commands. I like my volume response to be very fast on my remote. To accomplish this, i set my Volume IR Repeats extra high - forcing the "repeat effect" that we were trying to eliminate with the number buttons.
Regarding your TV tuning through all of the inputs on power on - that is a separate bug that I am going to work on separately. There are bugs both in the web admin and in some of the source code contributing to this. If you hit the [Change/Explain] link for your inputs, there is a checkbox "Send input select on toggle" (or similar) that appears if you have toggle inputs. This appears to me to be a setting for TV's that always start at the first input when turned on. On the 2nd page where you can change the order of your inputs, there is a second option "Send input select twice for the first input". This is for tv's where the input select brings up the input menu first, then subsequent presses will cycle through the inputs. The prolem is that there is a bug in the web admin that if you change one of the checkboxes, the other one changes with it. These should be two separate, distinct settings. My guess is that they are both checked on yours.
Hopefully it won't be too long and I'll get that part figured out. Its one of the few bugs remaining in the toggle handling.