I spent the afternoon rebuilding my CIT list (I took Lent off from the game, so I missed the post-crash fun until now). With the rearrangement of the settitle numbers, I can confirm the existing script is skipping quite a few, but I was able to pin (all?) down the gaps through my primary hero badger. In the interest of helping both other badgers who might be trying to find and fill their own gaps, and our no-doubt swamped CIT tech support, they are:
741: Socialite (Day Job accolade)
750: Entrepreneur/Profiteer (Day Job accolade)
1025: Disciple (history)
1034: Digger (history)
1035: Ghost Hunter (history)
1112-1120: the Striga, Talos, and Terra Volta explores
1121: Time Bandit (Hive explore)
1157: Trailblazer (200 badges achievement)
1158-60: the Croatoa explores
1161: Alumnus (history)
1162: Honorary Peacebringer (Moonfire TF)
1163: Portal Smasher (Quaterfield TF)
1164: Destroyer of Strength (Moore TF)
1165: Protector of Kindness (Augustine TF)
1177: X Times the Victor (accolade)
1178-85: the Croatoa defeat badges (three GMs, five factions)
1186: Geas of the Kind Ones (accolade)
My villain badgers aren't nearly as progressed and most likely some pure villain badges are being skipped that they simply don't have yet (therefore, I'd never notice). The only one I'm sure of is Thorn Robber, which I wasn't able to locate as any intuitive number. Also, of course, I can't speak for whether the script is missing any of the Issue 14 badges (answer: probably, not that it matters since you'll be earning them fresh), and there may be more gaps in the Day Job accolade list too (I still don't have all of those).