I had the same issues with my Directv box a long time ago. Here's what fixed my issues.
1. johnsfine modified all my learned codes by increasing the lead out time. That eliminated 90% of my issues.

2. My components were originally behind a glass cabinet door but, now, the door has been removed. I think the glass may have been defracting IR signals because of a bevel in the glass.

3. The IR signal from the Pronto and the blasters runs a bit too hot for the sat box so I ended up putting a piece of Scotch invisible tape over the IR receiver on the box.

Those three things made a 99% difference. I now have virtually no issues with my sat box.