Sound like You are experiencing IR issues. Here are few questions to help narrow down the problem:

1- What device are you trying to control?

2- Are you using any of the extenders (RFX....)?

3- Are the same macros commands the ones who always fails?

4- Is the component you are controling exposed to any source of "flooding" lights? (plasma's TV and fluresends lights are some time cultprits).

5- Have you try using the actual remote in IR modes aiming the device it self?

If you can, elaborate your responses and we help you get this taken care off!