All reputations are retroactive. If you have the rep now, it will count in the guild achievement. Also note that the reputations have to be separate. Having Argent Dawn at exalted on 8 members still only counts as one towards the achievement.

Also, don't forget that this achievement requires revered guild faction for any of your reputations to count.

Q u o t e:
I am experiencing the same bug.

My guild is currently stuck at 21/25 through the Ambassadors step of the guild rep achievements.

I have three of my own characters at Revered with my guild.

Character #1 has 21 exalted reputations and was the first to reach Revered with the guild. All 21 reputations appear to count.

Character #2 is Exalted with the guild. Has some of the same exalted reps as #1, but also has some that #1 doesn't (Shattered Sun, Sporregar, Mag'har, Violet Eye)

Character #3 is Revered with the guild. Has some of the same exalted reps as the other two, but is also exalted with the Scryers.

So, from these three characters alone, we should have 26 exalted reputations, even if I were the only person contributing.

Thanks for the report on this, we are looking into it now. Detailed reports like this are extremely useful.