I have the three STALKER games but they don't appear as Owned when viewing the games from the Sale Pack webpage. Aren't these the same games or has there been a subtle database change that flags these games as (somehow) different than the ones I picked up in the Summer sale?

What an annoying bug.
I have no problems; the first two show up as owned, the last one does not and it calculates package price correctly with the larger ~75% discount even when I put only Call of Pripyat into the shopping basket.
Are you sure the website sees you as logged in? There seem to be problems with that.

Yes. Pretty sure I was logged in since I could see my Library. Individually, each game's page showed as owned. But the pack page didn't show anything owned. I'll wait for the STALKER pack to show up again and see what appears then (assuming this sale runs as the past few have where all the packs/bundles appear one last time).