There is an alternative to SatoshiDice, it's BTCDice(.com), which is a S.D. clone but seems to pay out much faster and as far as I know hasn't had any problems paying out bigger payments. I'm still waiting on 46 bitcoins from SD which was over a month ago, so I've given up on them and made the switch to BTCDice.
If SD wants to pay me back the 46 bitcoins they owe me, then I would think about switching back to SD. Probably never going to get those back. IMO, SD should be listed as (not always paying back), but that's just my personal opinion.
SatoshiDice has paid back every bet sent to it. The only exception is bets which come from addresses that the player cannot access (ie - they send from gox, and gox doesn't send the bet from their account address, so it gets lots in the void - thus the warning on the front page).
Please post details of your alleged 46 bitcoins, and I'll get it sorted for you. But frankly I think you are mistaken.
I check the blockchain every day to produce statistics on SD. I post them to the
statistical analysis thread. As a by-product of this check, I get to see how many bets haven't been paid out. There is no 46 BTC bet outstanding, and never has been that I have seen.
Here's a list of the unpaid bets from the last run I did, about 12 hours ago, showing the bet transaction ID, the date, and the amount bet:
968a692ab98b1f275c635c76be003ab1db9740d0b62f338b270115342ca42f5b 09:39:19 Apr-28-12 0.10000000
a96a3cc6284df89c4d670722e6c2705b7d3709673be8e7207c53e02f35220d45 15:13:48 May-24-12 0.50000000
a83faeb7a346cd205143fbf68b6d261925993a111d5719ec7430ed673346dd49 16:12:00 May-24-12 0.50000000
8cc820a32ac2446f4087c67f5af06b1ed32a38f1ea9cacc22f931c96cb1528cf 16:13:54 May-24-12 0.50000000
ad4866a91ce24c624f3582aa87b19cd8e55361c31315b9d79d80084730697c14 06:33:05 Jun-09-12 0.10000000
bea477ad898c961642876207e65c0f7700581e3c839987e5de151dd640a7eaa0 17:43:56 Jun-15-12 0.04000000
c9cca3a9e5a1494cee2c87c950c1283f83d091920cb6e6749b3e5930d8d69ac2 09:29:03 Jul-07-12 0.01000000
72b97a20c5cee0b9f05b5203d0361263edb41b752a15e2838ac2b3b6789f74c2 11:31:37 Jul-28-12 32.00000000
6071357b4e24964f398de274e55c85cadaf33e1f54acaa284a7dfc23933feff3 17:47:08 Jul-28-12 1.00000000
18455d8b2020cef49579fa2f024375a43e242f4bb0c303cba526327944c65e46 17:47:08 Jul-28-12 1.00000000
802455195c92092bf863c82f77baec33e6f21fd8de2aa604826918d56e76d205 07:15:28 Jul-29-12 0.05000000
555cc5382acc939178dcb81cd83172984eec99b767f78bf05389c94657d01020 07:21:21 Jul-29-12 1.00000000
bb8d9eca3e807622e92472c4043a3573d4521c02927e563b58b8ad4a3d9d9173 07:28:15 Jul-29-12 3.00000000
eb3ee5f086b285fa40208257b59091b065d4f1f76b240a15d965da3790baa062 23:01:51 Jul-29-12 0.80000000
434cb9541a56d496e2d0a240f7ee75b4119317a5e32f79a71e5c5511289f1ebc 23:01:51 Jul-29-12 0.20000000
c508831ed64c7f4ff0d261d2971e38dab61e550e445ee3eb8f476d47cea0c12c 04:29:24 Jul-30-12 2.00000000
e7fe8ae530f9beaee6c0d8b89fb5d5aeee0a1a49a03be743e1bf796d66306c82 04:29:24 Jul-30-12 0.20000000
7bac881cf5bd745b944f3d1bec3934df70ef5b29a991b3ad8f6772ab853aa42a 22:47:06 Jul-30-12 0.05000000
e838d3a4494e91c747a3704fd3ee0f05840c576e960bd97a5947b54a301e364a 22:47:06 Jul-30-12 0.05000000
The first 6 or 7 are due to a bug in the version of bitcoin that SD uses to process its bets and may have been put right manually. The 32.00000000 BTC bet is by far the largest outstanding bet, and is the one this thread is all about. Here's a screenshot of the transaction, showing that the 32 BTC bet is "unspent":
If the bet had been paid back, win or lose, that output wouldn't show up as "unspent".
Edit: I just re-ran the stats and the same 19 bets are outstanding. This used to happen all the time, and fireduck would fix it manually. For the last month it's been a lot better until the rash of double-spends about a week ago.Edit2: When I re-ran the stats I hadn't run bitcoind since the last time, so of course I got the same results... Will edit again once everything is up-to-date.
Edit3: All up-to-date now. Only one of the 19 listed bets was paid out, the 14th one, txid eb3ee5f086b285fa40208257b59091b065d4f1f76b240a15d965da3790baa062.