Are your Apple codes learned from the remote that came
with the apple TV or from some other source? The codes
are problematic to learn and the remote that comes with
the device seems to be somehow paired. Using codes from
other sources can have inconsistant results

Try using the DCTxxxx (clean) codes found in the mega
code list 13 or 14 if you are using a Motorola Cable box.
The guide command needs editing (I somehow copied the
wrong code into that profile) but the codes should work
well.

Here is the Guide correction:
0000 006C 0012 0002 0153 00A9 0013 0054 0013 0054 0013
0054 0013 0054 0013 00A9 0013 00A9 0013 0054 0013 0054
0013 0054 0013 0054 0013 0054 0013 0054 0013 00A9 0013
0054 0013 00A9 0013 00A9 0013 0468 0153 0054 0013 0D13

If you learned them... try learning the command again
with good batteries in a clean environment (no LCDs, Plasmas,
CFLs, bright daylight....)