@Mularac...
Aye, the original game files work fine when I use them to create a new .dat file. It appears to be our modded campaigns (I've tried N:TAA and New Conflicts so far) that have issues.
@Arparso...
My intention is to create a whole new stand alone campaign. At the moment, I've removed some 90% of the alien presence plus any Human/NDF stuff that won't be required. In it's unpacked form, what I've got of the N:TAA campaign works great, so there are no missing files (especially the ones that it's complaining about). But yes, I'm afraid it will be a rather chunky download when it's ready.
Right then, I'm off to dismantle the patch and see what goodies are inside...
EDIT:
Found the problem... the .dap file was overwriting my tacticstypes.ini. Works great now
Maybe Nexus only sees a .dap file if there's an associated .dat file for it? With the game unpacked, it wouldn't find a .dat, therefore no .dap file, ergo no conflict. Only a vague theory mind, but it would fit the problem I had quite nicely.
Anyway, this one's solved so we can relax the grey matter, for a while at least lol