For flight points for multiple tickets to automatically post, the airline has to charge each ticket separately. If all tickets post as only one charge, you will only automatically get flight points for one ticket, and you will have to write in and request that they manually post the other flight points. (As an example, AA always does separate charges, but WN usually only does one charge.)
To add to this, Citi has a glitch where if your itinerary has multiple segments, you'll only get flight points for the first one (e.g. for DCA-ATL-CDG-BLR I was initially given all of 546 flight points). They'll fix this if you write in, but it's kind of annoying to have to do so repeatedly. If you don't want to deal with the hassle and are okay with getting credit for most but not all of your flight points, when you connect I suggest booking the longer segment first (e.g. SFO-JFK-BOS rather than SFO-LAX-BOS), all else roughly equal.