IR can be made to be 99% reliable with the right control system and a good integrator. The way this is done is by using a control system that does not require line of site from the remote to the device (TV/Blu-ray). What i mean is that your remote or touchpanel uses RF or wi-fi to communicate with a control processor or base station. The IR commands are sent from/thru the base station via IR emitters that are attached to the TV or Blu-ray player or whatever.

What this does is it gives you a very reliable wireless connection via RF or WI-FI between your remote or touch screen and a very reliable wired connection between the processor or base station and the TV or Blu-ray player or whatever. Now it doesnt matter what room you are in or where you point the remote. Your commands will be sent to your devices.

You mentioned your pronto. Are you using IR directly out of the pronto? Or are you using an extender?

If you are using an extender and still having issues with missed IR commands then my advice would be to look at your macros and make sure that you have your delays between commands adjusted. As an example. TV ON and TV INPUT2 would need a long enough delay between them so that the TV can actually turn on and accept the INPUT command.

A macro would look like this...

TV ON
Delay 5 seconds
TV INPUT 2

To give you an idea of how different delay times can be for different TV's i have a 14 second delay at one clients house for her 19" samsung LCD's. Most TV's will take an input command after 5 seconds. So this sort of thing needs to be tweaked on site.

Another thing to look at is to make sure that the IR ports are routed. A. to the TV B. to the Blu-ray player etc. And (if possible/available) shut off the IR blaster.