for the first one: I get a similar error. I load the .sof file with Quartus and then click the connect button in the control panel. A bit more work, but it'll get you there (I think).
the second one: Do you have the right device selected? There might be a problem there, also you should make sure the programming switch is at the right position. (refer to manual for this. I think it is run.
and for the thirf one: search this forum. I believe I have seen this before. It could be a setting somewhere.
note: These are possible solutions. But since they all have to do with programming/sof files It could be there is a common problem for these issues.