The GOG version should be 1.0.0.9. Are you sure you got the latest patch?
I was 80% through getting v1.0.0.7 when GOG Downloader stalled. I checked the site and they'd take it down and put up v1.0.0.8 instead. So I deleted the partial download and started again.
You're right that they have since provided v1.0.0.9 -- and thankfully a patch to it this time.
Btw, isn't it easier for you to just use GOG Galaxy, doesn't that download just the files that have changed?
Probably. I guess I'll try it out in a VM. I've just found such game managers to be counter-productive in the past:
I haven't tried GOG Galaxy, no. Steam / Origin's tray executables tended to make simple things complicated, slow boot time, hog resources, download updates for the client itself silently, wasting monthly data I couldn't spare, and generally be all pain and no gain. Maybe GOG Galaxy is better :-)
It certainly would be an attractive offering if it was able to automatically transfer just the delta for installed game(s), and if the quota overhead for maintaining the Galaxy client itself is reasonable.