If you look at the signal strength meters (Services>System Setup>Signal Test) You will see two meters one showing strength and one showing quality. chances are that the quality meter may be a little down? They should both be above 80%. When the dish is aligned it is aligned in two axis and four bands are checked, all of which need to be above 80% Horizontals are set on the dish main bracket and then the verticals are tweaked to give maximum signal quality. Chances are your dish is slightly misaligned and therefore is missing part of the signal. Consider the distance between your dish and the sattelite - a very small angular deviation at the dish could lead to missing a satellite by miles..
The only way to get a proper check is by using a proper Sat Meter - unfortunately Sky will charge for that privilege
(BTW I was lucky enough ? to work as an installer for a couple of years
)
Also if you connect to a phone line then remove th emains lead from the back of the box and put it back in whilst holding the backup key down (on th ebox not the remote), you will force a software upgrade on your box (it will take around ten minutes to download) which will upgrade your software to the latest OS version. This can be an issue on boxes that have been unplugged from the phone line and can cause problems with the on-screen programme guide.