As Brotoles and sharpman pointed out, I also noticed that when I use the Downloader to verify my downloaded games and check for updates, it adds the installers in a suspended state and "redownloads" them again. It looks like resuming a paused download, it skips the parts that are already on my disk and sometimes finishes instantly and sometimes it downloads some parts again.
This can lead to corrupt installer files, as I noticed with Fallout Tactics for example. I think that happens when the Downloader downloads parts of an installer it thinks are missing or out of date again.
As I have a huge collection of games from GOG, and frequently use the Downloader to update it, I now don't know which of my files are corrupt and which are not. That's bad :-( Checking them all manually would take way too much time, especially if I have to run the setup for them all and sometimes there seems to be no file integrity check before installing.
When you add a game to the downloader to perform integrity check, it will check each chunk and compare it's checksum. If the checksum is invalid, it will re-download this chunk.