I broke the reputation cap today answering this question, but it got merged some time later and my answer did not make it (as it became redundant then).
I briefly mourned the hundred rep points I lost in the process, triggered a recalc and went my merry way. However, I later realized the system still thought I was above the rep cap, so I double-checked the reputation page and it was up-to-date. It remained up-to-date throughout the evening, but the site didn't catch up.
Now, I understand why the site doesn't catch up with reputation increase in this particular case, but I was under the impression that a recalc would completely synchronize the site's state with my current reputation. I don't really understand why the reputation cap is a special case here. (My best guess is that the site maintains its own cached state for efficiency, and that cache is not invalidated by recalculations.)
Is this behavior by design? Can it change? Should it change?