When I saw Suffering on GoG front, I was confused; since I knew this game had been given away as freeware by the developer

http://www.gamershell.com/news_60914.html

I played it a little and never thought it was a good game at all, mostly deserving being abandoned and given away for free (however harsh that may sound, I didn't intend that, sorry).

Obviously, when checking for the source of this, I also realised the downloads were no longer up, also not on any other site that I know of an trust to be legit.

Does anybody know what happened and why the game is being sold again?

This is the official USAF giveaway website (archived): https://web.archive.org/web/20120409193223/http://extcamp.doublefusion.com/US_Air_Force/Game_Download_Sponsored_by_Air_Force.htm

This version contains advertising and requires internet connection. Servers are certainly down now. I don't know if it is possible to patch DRM out.
The GOG release is superior for all intents and purposes.

there is a new copyright holder if GOG was the new copyright holder but i doubt it otherwise it would be 6€ or 8$ or 4£ because of now new copyright holder its inflated and yes the sound is now playable it seems just seen on YouTube will buy it later due some financial problem :)