I had a similar problem with an x-box 360 elite and msc-400. It was hit and miss with powering on and off. I tried different button repeat settings and increasing the IR output delays etc. Nothing seemed to be reliable.
I eventually repeated the command twice in my macros in the msc-400.
XBOX 360 (MSC400 (Home theatre),p-off)
XBOX 360 (MSC400 (Home theatre),p-off)
I do the same for turning it on.
It's the only component in my system that I need to do this work around.
I'm sure there must be a better way; but this works every time for my set-up??