A system-wide recalc happens occasionally, for example when the rep rules are tweaked (like this). Since December 2010, you can also trigger a recalc manually, following the instructions on your reputation report.
Other than that, a rep-recalc can be triggered on your account by ♦ moderators:
- on request
- if we've done something like merged your account(s)
- if there is a suspicion of "inappropriate activity" that has resulted in one or more posts being deleted
In most cases, a rep recalc is nothing to fear. I've seen rep recalc result in increases as many times as decreases.
Re your last point... a regular system-wide recalc possibly wouldn't be a bad thing, but I have no idea how much impact it has on the system. Per-user it is pretty cheap (it'll process me in about 1 second - I just did it, and gained 2 rep! woohoo!)
A few known causes of discrepencies (there may be others):
- a post you had previously gained/lost rep on is deleted
- there is a "feature" that can lead to over-the-cap (i.e. 201+ points in a day) users losing 1 point repeatedly - recalc claws these back