This bug and reproduction steps below are based upon my knowledge of how the iPhone app works. I may be missing a critical piece of information, but based upon my tests I can reproduce this issue repeatedly on my iPhone4 using the current version of the Eye-Fi iPhone app (version 2.0.88). If the same logic is used in other apps, it may be effecting those apps as well.
1. Take two photos using an app that has it's own lightbox such as Camera+. First photo A, then photo B.
2. Using Camera+, save photo B to the iPhone's camera roll (which can be viewed using the "Photos" app).
3. Open Eye-Fi app for iPhone and sync photo B.
4. After photo B has been synced, use Camera+ to save photo A to the iPhone's camera roll.
5. Open Eye-Fi app for iPhone and attempt to sync photo A.
Photo A should be synced.
Photo A is not synced.
My guess as to the problem is that it seems the Eye-Fi app only syncs photos with dates newer than the last image successfully synced.
Update the iPhone app to sync all photos which are not already synced.