In today's Dec1108.puz (New York Times), right clicking on the last character of 13 down and entering a 4-letter word (TURN), then moving on by any means (Enter, Return, Clicking elsewhere) places the entered characters in the box of the last character of 63 down (63-D-3, 69-A-3) although a similar entry in the top right hand corner (1-A-1, 1-D-1) worked perfectly.
I have zipped the puzzle, saved in its broken state, and emailed it to you. I can still do the puzzle just leaving out those 4-character inclusions.
Thanks Adam, I just reproduced the problem myself. This is a serious problem and it looks like it was introduced in 1.1.3. I will get on making a fix and post an update here ASAP.
I would delete the corrupted puzzle and start over from scratch. Unfortunately, once it got messed up there isn't much Black Ink can do to salvage the wreckage.
I'll publicly release it later today if it gets the OK from you.
Thanks, I suspect it's not exactly the same problem, but you've probably discovered a related bug. I'll look into trying spaces in the multi character entry.