There is a bug in subaku. I am very sorry about this. It does not have any impact on normal play, but does prevent custom puzzles from working correctly. The fix has been submitted to Apple and will probably be live in a week. I will put up the promised daily puzzles for this period in one big lump once the fixed version comes out.
If you are curious about the bug, it is a pretty goofy one on my part! Basically here is your coding pro tip for the night: NSStrings and NSNumbers are not the same thing! Obvious, but when subaku loads up with a custom puzzle URL it takes the puzzle string, chops it up and dumps it into the engine. It normally gets put in as NSNumbers, which I get the integerValue of to manipulate them through the gameplay.
Well, I forgot to turn the NSStrings into NSNumbers. This was not a big problem as integerValue works the same for both of them, so everything worked right except for the match checks. It ended up going "Strings and Numbers? These do not match!" and then would not clear out the right tiles. I missed this bug because once the tiles change they get stored again as NSNumber and there is no problem. So not only was there a goofy mistake on my part but a bit of poor testing. I learned a lot here, and thankfully it will not do much towards the main game.
Thanks for your understanding and playing subaku.