The server can pregenerate about half of the potential client seeds. In 999dice's case that would be 32 bits which would take about 1 hour on an Intel ivy bridge.
I tried clicking their checkbox for manually entering client seed but nothing happened. How can they be limiting it to 32 bits? That's just 4 bytes.
This again could be an innocent mistake, but really, why would you limit the client seed to something easily bruteforced if your intention was to make a provably fair game?
The reality is that the more a site strives to reach 100% provably fair the more likely they are being fair.
If you copy an existing provably fair site and change the provably fair system in at least 3 different ways to make it less provably fair, then what are the odds that you made all three changes innocently?
1) change the server seed every roll, requiring the user to change their client seed if they want provable fairness
2) hide the server seed hash behind a button so you can tell which rolls are possibly being verified and which aren't
3) restrict the range of possible client seeds to just 32 bits
It's still possible that the site is running an honest game and it's just unfortunate that they made three unfortunate mistakes in their provably fair system. It's also possible that they knew full well what they were doing, and used it to cheat careless players.
Their theoretical edge is 0.1%, but their actual profit is closer to 0.4%, 4 times higher than it should be. That's also possibly entirely innocent.
Like I say, I would recommend not playing there until they fix things.