Hmm, at first glance, there doesn't seems to be any inconsistencies here:
- The 2nd link shows an entire "chunk" of received reputation, whether it's bounty or something else. Thus the green color like other entries.
- The green background is probably selected when mentioning "important" events which include acceptance as well as bounties.
- The 3rd case is also "chunks of reputation" but uses no highlighting at all - so why should it make an exception for bounties?
- Note that even in the 1st case, only the entry for a specific question that includes the bounty is blue, the top-level "chunk of reputation" entry is green:

...Oh, I see what you're driving at: the blue entry in the 1st case has question granularity, like the green entries elsewhere.
- Well, the difference here is that the 2nd and the 3rd lists are one-level. While the 1st one is multi-level and the blue entry is on the 2nd rather than the top level, thus invisible by default for all but the latest 3 days and even there, is clearly visually separated from top-level entires (different sizes, different fonts, different indentation... the guy who designed this is good!).
- The reason here appears to be a UX-based one: if the top-level entries were in multiple different bright colors
- It would be distracting
- It would have negative usability. For a top-level entry - "reputation chunk" - green color means "reputation gained", red color - "reputation lost". What would blue color mean for the purpose of the bottom line? Nothing. It would only throw away this information coded by color, forcing one to read the number.