I'm not certain how to solve your specific question, however, I do have some thoughts about how you might rework your design to improve the quality of your application and eliminate the problem you're experiencing.
While some of the guys who are component masters may be able to help you hack this functionality, I don't usually think of a contentplaceholder as a way to swap content in and out for "one page". The entire point of a master page is to encapsulate the XHTML which is consistent across all pages of your website so while it let's you swap out content from page to page, the situation you note is a little different. You don't really gain anything by using master pages in your situation.
Also, while AJAX and Flash have made it very trendy to build one-page applications with all sorts of functionality built in (printing, bookmarks, linking, etc.) I've never like that application architecture. These are all features that are built into browsers much more flexibly and efficiently; it's also functions that are standardized through the browser making them much more intuitive for your users because they do "exactly" the same things on every website to make them work; your application will need to reinvent the wheel and it will still be confusing for people because they'll have to learn how to make things work the way they want on your site from scratch. A one page website, is quite literally impossible to navigate and impossible to bookmark effectively.
I'd recommend leveraging the advantages of master pages to build a multi-page site. It will eliminate your current problem entirely, because you will simply build each function into a separate content page. The template code in the master page and the styling in the CSS will still make it appear that they are on the same page if that's how you set it up. So you can achieve the same effect. Moreover, people will be able to bookmark the page they need if they have to stop part way through the process, and you can navigate people around the site normally with links or using page redirects which are well documented across the net. I think that's a much better way for you to pursue this application than trying to manufacture complicated new code and figuring out a way to shoehorn a solution into it. I really think this is an application design issue, not a lack of code.
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