I'm afraid that the patch has a bug: in certain situations some of the evil ninjas are invisible, making a few levels impossible.
We've already figured out what the problem is, so it should be patched soon (sadly it seems to take us 1-2 weeks to actually get through cert without issues though).
I'm really sorry about this "fix a bug, create a new bug" pattern that all of our patches suffer from. It's really embarrassing! :/
The good news: we've found a new programmer, and they've been working on porting N++ to Steam for the past month or so. There are still a few more months of work -- we want to add all of the planned post-launch-update stuff that got put on hold when our team imploded -- but we will definitely be bringing N++ to Steam. We're still looking at other platforms too.
Anyway, thanks for your continued support... and please keep letting us know if you find any new bugs.