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I had noticed the same thing on a number of my pages.  Like you we got an initial fluctuation for our main keywords after penguin, but after time they stabilized, and many of them returned to the #1 position (even though I still notice jumps of 3-5 positions daily). But where we really seem to have lost the most traffic were the long-tail keywords.  Now, these were not necessarily keywords I had optimized for specifically, but they were ones we had ranked for in the top 5.  For example if I optimized for "nice big blue widget" I was also showing up at or near the top for "nice big widget blue".  Now I am nowhere to be found. It seems like google stopped giving credit for related words.  They are only ranking for the specific words you optimize for and not for anything else.  Not sure if it is only me, but I have noticed this on a number of our sites. Not sure if it helps, but just to let you know you are not the only one seeing this.

Thank you for your reply, the sub domain contains an extensive library of xml schemas, http://bit.ly/aOEsG7 and is more a referance point for he developer community who may use our product (xml software tool)

I have a few questions Andrew. You want to target download.xml as a keyword and you do, but currently rank on page 2. Therefore you want to increase this rank to page 1. Why do you need to set up another page? Why is the current page not suitable for your needs, and can it be optimized better for this keyword? What is your intent for the new page? Why do you see a need to have a second page to target this keyword? You say you want to rewrite the URL. Are you saying you want to re-code the URL or do a re-write rule on the URL in the .htaccess file? With the information you have provided, I see no reason to create a new page, but simply optimize further the page that is already ranking for this term. Perhaps running it through the on-page report  card and building some inbound links with exact anchor text.