I think I have the same stb, and this happens to me sometimes. As far as I can tell (theory only) the stb has two sets of codes it can listen to...depending which one it sees first it will react to that set of codes...so we have to make it see the mce blaster and NOT the mce remote...
1) unplug stb for a few seconds
2) plug it back in, wait for it to boot and wait for the spinning ntl logo (bottom right "starting" to disappear)
3) cover the front of the stb with something (radiotimes come sin handy) so that the stb receiver cannot see anything external besides the mce ir blaster)
4) change some channels using the mce remote, the first few changes will do nothing, then slowly the box will start listening to the mce blaster exclusively
To verify you have to done correctly, change channel using the mce remote. As soon as you press ch+ or similar, watch the stb. The lower of the three status LED's should NOT flash in reaction (i.e. the stb should not have recognised the mce remote). Once the blaster starts flashing then the lower (third) of the stb status led's should flash in recognition. This means the stb is listening to the ir blaster, and not the actual mce remote.
I may have to repeat this procedure occasionally as sometimes in the rainy weather my box has a habit of rebooting...
The correct codeset was pace c1060, but with the mce updates they have added a category "ntl"..not sure which box it is under that category...but pace c1060 set to slowest (plus my trick above) gets my box working everytime. I am on the "purple" firmware from ntl.
hope this helps