Thanks ixion. I've looked at this again, and I think you're right about the checked letter in 21dn/27ac. The same issue applies in 6dn/10ac and 9dn/10ac. The instructions are poor - I had assumed all the non-Playfair words in the grid would be legitimate words. I'm not sure what you mean by changing the definition though.
31ac is a Playfair answer, so it will need to be encoded before entry. Presumably, it will then fit with the last letters of 21dn & 25dn.