Deciding when house rules fix a problem and when they break balance

We introduced a house rule to speed up the slowest phase of a game. It made the first session more enjoyable, but by the third play everyone was exploiting a strategy the original rules apparently prevented. Now we're debating whether to tweak the tweak or just return to the published version. When do house rules genuinely improve a game, and when are they hiding a part of the design we didn't understand yet?