As it has repetitively been explained, Eligius is special because it doens't -have- any money. It pays you directly from the generation transaction. Therefore, it can only pay out as much as it mines, as luck allows.
Huh? What's this whole manual transaction thing about, then?
When the system goes into failsafe mode, all transactions go into a cold wallet controlled by Wizkid057 and (I think) Luke-jr. When the database gets caught up and/or the error resolved, they initiate a manual payout. Also, as I understand it (and I could be wrong on this) they keep some reserves in there to take care of problems.
In any case, I've never seen it go more than three days of being borked up before Wk does a manual payout.
Right now I'm mining alts, but when I directly mine BTC this is the only pool I use. They've always been johnny on the spot fixing whatever goes wrong, and aside from the recent NMC thing that's still ongoing, it's always just been the stats and payouts. I've always gotten what I expected, except once when it was a bit more than I'd calculated

I'm assuming the error was in my math.
Don't stress it too much. These guys are honest and have demonstrated it over a fairly long period of time. I'm in the camp that wants them to initiate mandatory fees, as I think that they ought to be well compensated AND have time for maintenance. WK has indicated that he is not in favor of this, and it's his baby, so I'll just voice my opinion and continue to donate 1 percent whenever I mine here.
I'm not complaining. Making payouts in real time would be quite a feat. It wouldn't even really be possible because there's a limit to how many addresses you can put in the coinbase transaction.
I'm just pointing out that Eligius
does have money.