We seem to get a request to explain the bug on every second page or so. It is explained 2 posts over yours, here's the short version:
Windows Vista/7/8 are saving the compatibility setting for every executable in the registry, all in one folder so to speak.
When you de-install a GOG game with the bug, it deletes all that information, not just the settings for the game you de-install.
Nothijng too bad, and you do not have to re-download and install all your games, only if you want to keep all your GOG installers on you hard disk like me and some other people.

Thanks a lot. Sorry for not noticing it was answered already :/.

1 more ignorant question. games with only 1 exe and no .bin files apparently don't verify now from what i read? But they now have a digital certificate...? What's the certificate do and how does it help me tell if the file i downloaded is correct? Sorry if my question makes no sense and i'm being completely ignorant.

Letting Windows check if the certificate is correct seems to be GOGs new method to verify smaller installers.
You do that by right clicking on the exe, choose Properties. Here choose the digital signatures tab. Click on the one signature in the list and click the Details button. Now it is verified that everything is signed correctly, that can take a minute or 2 for big files depending CPU/harddisk/etc. If there is something wrong with the file you downloaded it will say that the signature is not valid.
Sorry I can not post what it says exactly at the moment, the PC I'm using right now is on German language.

Just a heads up, Invictus still wipes your compatibility settings when you uninstall it.

Edit: Shogo too.

Anyone can check out this for himself with some basic knowledge of the command prompt.
You use this tool Inno Setup Unpacker to extract files from the gog installer.
http://innounp.sourceforge.net/

example command line: innounp -x setup_system_shock2_2.0.0.9.exe install_script.iss

Open install_script.iss with any text editor and search for this lines.

Root: HKLM; Subkey: "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers"; ValueName: "{app}\shock2.exe"; ValueType: String; ValueData: "RUNASADMIN HIGHDPIAWARE"; Components: Component0; MinVersion: 0.0,5.0; Flags: uninsdeletekey
Root: HKCU; Subkey: "SOFTWARE\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers"; ValueName: "{app}\shock2.exe"; ValueType: String; ValueData: "RUNASADMIN HIGHDPIAWARE"; Components: Component0; MinVersion: 0.0,5.0; Flags: uninsdeletekey

uninsdeletekey is culprit. It should delete just the value instead of the whole key.

TET has informed us that the huge silent change has just been an update of "a billboard graphic in the installer (those little images that display while you install the game)", not the exprected bug fix.

Here: http://www.gog.com/forum/general/gogs_massive_silvent_update_game_list/post39

Well that's not very true, because most of the games that were silently updated don't wipe my compatibility settings now when they used to.

Edit: So they must have went ahead and fixed it while they could, and are still making a method to not redownload everything? Who knows.

obviously, the dev-team made some changes , but for them it wasn't necessary to let us know.

now , i don't know from what u said + what said / know TET what all the changes.

no real announcent, so every customers who care about updates / backup games are in the fog

i'm currently checking my whole collection (250+ games, minus those in the list) to see if no more games have been "a bit" updated T_T

i asked , ff it was the only updated , but he was already off-line

For some reason, SimCity 2000 doesn't seem to have a Graphic Mode Setup.

You are probably right, but as far as I know, Invictus and Shogo haven't been updated (yet?).
But we are just guessing. Why don't we check the changelog?

Good idea!

...wait...

invictus got an update, the downloader wanted to add data to the file i have (which lead to some issue with the final file ....)

it will be included in the list , i just need to finish the checking...

the changelog ?; in another dimension i guess....

Locomotion got an update.

ok my list got a massive update (it's almost the double now T_T)

basically almost all the games in my collection with a v2 installer got an update , those who escaped it , will probably got one sooner or later..... (inluded locomotion, thanks for the notication :))

2 games got a patch (demon's stone + legend of grimrock , same patch number , different checksum -> i checked the certificate of those , there're differente from those i have). Maybe it's for fixing the uninstall bug (i don't see why doing this with patch otherwise)

there're some games in my collection i never got the opportunity to d/l , because of this big mess. :
so probably some ot them got an update , i can't do anything atm for those. and when i will have finished the task at hand , they will be updated...

oh yeah , final note : check the patch too (since i found 2 of them with a different checksum... at least it doesn't take a lots of time.)

that's all i guess

This is the difference.