Give the GOG downloader time. It will show only one setup file in the interface, but it will actually be downloading two files, so you need to be patient while it completes. The files should be:

setup_sw_kotor2_2.0.0.2.exe (34.3 MB)
setup_sw_kotor2_2.0.0.2.bin (3.06 GB)

Both files are required.

The gog downloader is showing as download completed though, and checking the download directory shows it has only downloaded the 34MB part 1.

Remove the downloaded file completely, make sure you have GOG downloader mode on in your browser, then click the installer link (in your browser) and try again. If the same thing happens, you need to contact support.

Yep, tried all that - still no joy, so I've contacted support. Thanks anyway,

I have exactly the same problem. Tried with and without gog downloader, and from different operating systems to make sure it's not a problem on my end. I also tried the "refresh" link https://secure.gog.com/en/account/refresh/
I wrote to support, but maybe it would speed up things if they get more than one message on this topic. Probably it's very easy for them to fix, looks like a file has accidentally been moved to the wrong place or something.

edit: for some reason, the spanish version works.
the file is actually called setup_sw_kotor2_2.0.0.3-1.bin instead of setup_sw_kotor2_2.0.0.3.bin
however, manually editing the link to get the English version doesn't work due to gog's security mechanism.