1: You are clearly not receiving one or more muxes well enough. See
here for details of the six muxes. I think you'll find that you aren't getting all of at least one of these.
It's an aerial issue. It may well be that your transmitter used a broader spread of UHF channels (frequencies) for Freeview than for analogue, and this would indicate the need for a wideband aerial. The
same website gives details of the aerial type (group) needed for each transmitter. If it says W then that's wideband and it's probable you don't already have one of these. Or it could be symptomatic of the two aerials - see below.
2: It doesn't. It will scan for channels using everything that comes down the wire. Given two aerials this might mean
- it finds some channels more than once
- signal from one transmitter intreferes with the other and prevents reception of some channels. An analogue programme on a UHF channel the same as or next to a Freeview mux from the other transmitter would prevent reception
- two aerials might cause a double signal which would appear as ghosting on analogue, but might make Freeview unreceivable.
Note that signal "cleanliness" is paramount for digital reception. Even if you have a strong (but "dirty") signal you might fail to receive.
I'd say an aerial rework is needed. If you want to keep access to two transmitters, you should use two separate downleads and physically change over as needed. Note that, on Freeview, this will need a channel rescan every time.