I can confirm that the latest patch is what causes the problem with Seeker. I played through the game for the first time on hard mode on my regular Xbox. I picked up the intels in the level but didn't get notification for it and the end of the level showed - for secrets.
Once I finished the game and started looking for solutions to the Seeker problem, I heard a lot about the patch problem. So I took my save game and then played the level on a second xbox that I disconnected from the internet so that it wouldn't receive the patch.
As I played through the level and I came upon the intels, sure enough it gave me the "you have found a new secret" message after collecting them. Once I had both of them I earned the achievement. And those two in the level are Intel 05 and Intel 08 unfortunately.
The strange thing is that I have since taken that save and booted the game back up on the original xbox. The game shows the achievement completed, but if I go into the overall stats on that console the secrets are still only 28/30.
So if you only have one xbox, sounds like clearing out the cache on it and then making sure that the console isn't connected to the internet until after you earn the achievement is the only way to get it until they release another patch for the game (if they do).