No, it's not a black mark. There's no particular reason not to apply now, if you're ready.

Paul, is being accepted in another 'incubator' a black mark? We submitted early this time though.

No, not at all. Lots of the startups we fund also applied to and were offered funding by other YC-like organizations.

That's good to hear - we'll submit an application this round. Thanks for the quick response :)

Apply late so you can have that awesome story of being the company that barely decided to apply after the deadline and then went on to be the next Facebook ;-)

Go for it. So many places set an arbitrary deadline because they know a few will come in late, so they build in a buffer. Plus you never know, someone may back out for some reason and they need another one to round out the numbers.