When I get an upvote, I get a green bubble:
These can merge to show total rep across all the sites:
That shows that I got + 40 and -1 (I downvoted).
This however, doesn't exist:
You don't get bubbles for - rep.
What this means is, if I offer a bounty for 50 (e.g. here) and then get 2 upvotes (I did) I don't see the bubble. It would have to display this:
That's the bounty (-) and upvotes (+). It can't show this.
At the end of it all, because it isn't showing me - rep, I don't see that I have any rep gains here because they cancel out.
Just to be clear, it is only when the bounty and upvotes are on the same question that I don't see upvotes... For example, just here I got the +5 notification for this question being upvoted
Upvotes and downvotes etc still cancel out, and it is only displayed if the over all is +ve, but bounties are not included in this measure. Either it would show the -40 or it would just show +10 and completely forget showing the bounty.