I updated to 4.0 and am having the same problem with the file extension and date stamp. I saw your reply about adding the extension myself so I probably should explain the workflow that is causing the problem.
My text file are named like this CATEGORYx - FILE NAME - YYYY.MM.DD.txt . Because all my files are named like this and because I'm creating text files for certain categories on a regular basis, and on multiple devices, I've created a TextExpander snippet for file names. I have a snippet for each category and the snippet places the cursor where the file name would go, so in other words the cursor is placed in the middle of all that text. However, in all other situations, be it in Byword, nvALT, Drafts, etc. I don't need the .txt extension at the end of that snippet because those programs add it for me (or don't show it at all). But with this Alfred workflow when I use my snippet the DD gets cut off in favour of the .txt extension.
I'd like to try to get around this without having to create a whole new set of naming snippets just for Alfred.