Add [Variant "Chess960"] to your PGN, for example after FEN. Then import wizard will treat it as Fischer random game rather than a standard game.
Import bug
Including the PGN tag [Variant "chess960"] solves the import problems, and as far as I've tested, it fixes the castling bug, too.
If a field for [Variant] is added to the Game Details panel in the import wizard, 960 publishers could be wholly in business.
The trouble is that the Rules dropdown doesn't always "stick". But your recommendation about adding the Variant tag ensures that it hold, it seems.
Oh, you mean PGN import.
It will import as standard game unless there's a Variant tag. The import will choke on castling, so you would have to change the rules and then manually add the moves including castle moves (may need to delete these first). It's way more easier to add Variant tag when you import.
But it should work okay for FEN imports.
A different kind of import bug — if some 960 files are imported with castling, an ambiguous rook move breaks the import wizard. Steps to reproduce (verified in three Mac browser, plus Firefox in Linux):
Homepage
1. From Home menu, select Blog
Blog
2. Click Create a Blog Post
Submit new blog
3. Enter a title 'import bug'
4. In the Body panel, click the Insert icon
What would you like to create?
5. Click 'game or sequence' radio button
6. Click 'Continue'
How would you like to begin?
7. In the PGN field, paste this PGN
[Event "?"]
[Site "?"]
[Date "????.??.??"]
[Round "?"]
[White "fgh"]
[Black "000"]
[Result "1/2-1/2"]
[PlyCount "18"]
[SetUp "1"]
[FEN "bbqnnrkr/pppppppp/8/8/8/8/PPPPPPPP/BBQNNRKR w KQkq - 0 1"]
1. b3 b6 2. c4 c5 3. Nc3 Ne6 4. Nd3 Nd6 5. Qa3 Qc6 6. Bc2 Bc7 7. Bb2 Bb7 8.
O-O-O O-O-O 9. Rde1 Rde8 1/2-1/2 {Here is an import bug. 9. Rde1 and 9...Rde8
don't get imported by the wizard.}
8. Click 'Continue'
Game Editor
Expect: The PGN as imported
Get: 9. Rde1 and 9...Rde8 missing from the move list