With some boxes without the ability to limit the channel search to the
frequencies used by an individual transmitter a problem can arise where
the aerial can pick up signals from more than one transmitter - the one
you want and the and a much weaker signal from a more distant or
different transmitter.
Say, BBC1 was on transmitter channel 21 from the transmitter with the
very weak signal and on transmitter channel 31 from the desired
transmitter with a nice strong signal. The box starts scanning from
transmitter channel 21 and immediately finds a signal, albeit weak, and
populates the BBC 1 slot in your TV channel list - the box keeps
scanning and when it gets to transmitter channel 31 finds another BBC1
but because its already populated that slot perhaps puts the duplicate
much further down the list of TV channels. You now have two instances
of BBC 1 in your channel list.
Is this the case you are seeing? Scroll through the complete list of
channels to see if there are duplicates much further towards the end of
the list of TV channels that don't give you the weak signal message.
I don't know the Manhatten box and how it scans for channels but in the
past with various boxes I've owned since digital TV started I've had to
resort to manually tuning for each Freeview MUX and/or putting an
in-line attenuator in the aerial line during scanning to make the weak
signal from the "wrong" transmitter even weaker so it's not detected by
the box. The attenuator is then removed after scanning.