In the last couple of weeks, Eligius has gone from a pool of about 225 TH/s to a pool of ~500 TH/s.
As the hashrate of the pool increases, your individual share of the pool will decrease unless you add hashrate proportional to the growth of the pool.
Therefore, as the pool grows, your individual payout per-block will drop, unless you increase your hash power, as above.
However, since the pool's overall hashpower has increased, the pool will find more blocks - and the increase in blocks * your new smaller payout per-block will even out, and your overall payout per day should not be significantly different - and the variance in your payout should be less - that is, your payout should be more predictable in a given time frame.
If you are finding that you are actually making less BTC per day, then there may be a problem - but it is expected that you will see a smaller per-block payout as the pool grows larger.