This problem (see
this thread) has proven impossible to solve (at least for me) via reverse-engineering the MOBI format variant being used by Amazon. Therefore, because I consider the problem a serious impairment of the Kindle 3 user interface, I have developed a software engineering solution which works quite well. I'm sharing it here for the benefit of others who want a solution to this (for me) vexing problem!
The solution consists of using the Calibre command line interface to create a standard OEB version of a downloaded periodical and then processing that with Amazon's Kindlegen to produce the Kindle-compatible MOBI file. I have automated this process with a Windows batch file. If you want to schedule downloads you can use the Windows scheduler to run the batch file on whatever schedule you wish.
The batch file edits the recipe you specify to add some code to make the Calibre OEB output work properly with Kindlegen. You don't have to worry about what those changes are, and no changes are made to your original copy of your custom recipe (if you're using one) or the built-in recipe (if you're using one of those). The changes are made and stored in a temporary recipe file every time you run the batch file.
The batch file will optionally add the generated files to the Calibre library and/or email them to your Kindle (or anywhere else you choose).
The disadvantages of this solution are (a) you have to download and install Python and Kindlegen on your PC--but they are both free and easy to install; (b) it runs outside of Calibre; (c) you have to reference built-in recipes by their files names in the Calibre release directory; (d) it's a PC-only solution--sorry, Apple people; (e) the masthead feature doesn't work--a limitation of Kindlegen; (f) I don't have time to provide hand-holding support for this.
The advantages of this solution are (a) it works--problem solved; (b) it uses whatever release version of Calibre you're running, including the built-in recipes, so you don't have to do anything to stay in sync with Calibre.
There are complete instructions in the attached zipped folder for setting up and using this solution. If you find bugs please let me know, and I'll post updates in this thread as necessary.