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In my experience, Freeview reception is not particularly good as, during the transition from analogue to digital, the transmitters need to power both digital and analogue signals, therefore, the digital signal will be of reduced power. During this transition period, digital signals will be lower strength.
Once the analogue signals go off, I anticipate better digital reception. Unfortunately, in our area it may not be until 2012!
In our area, even with a rooftop 'digital' aerial, our digital channel signals still break up regularly, even in times of good reception. Without the rooftop aerial we'd receive nothing.
Old analogue aerials are 'narrow band', designed to pick up a limited range of frequencies. Which is why they often pick up some digital channels and not others.
Also check your downlead. Analogue will work with any old coax, digital prefers CT100 (low loss, as used on satellite receivers). Make sure your coax plug is nice and tight too.
If it is one that plugs into the mains try turning off the power (I know it sounds strange)
Sounds like you already had a strong signal, by amplifying it you overloaded the tuner in your set top box.
Once the analogue signals go off, I anticipate better digital reception
Digital interferes with the old analogue signal, so for now its broadcast at low power. You are quite right, once analogue is turned off and the power turned up reception will be much more reliable.