Sorry about the late reply.
Just to confirm, yes, when I say "import manually" what I actually mean is I re-download the mod using the "download manually" option on the Nexus.
As far as I can tell, the suggestion that the mods are corrupt downloading through MO on occasion seems to be what I am experiencing, as when I try to open the MO - downloaded archive with 7zip it gives me the standard "cannot open this archive" message.
Also if DanimalTwo is correct and its happening with manually downloaded mods as well, that seems to suggest that it's a Nexus issue not delivering the downloads correctly as appose to an MO issue.
So really I'm just re-iterating what other people said, but yes, I agree with the observations made.