I too am having this problem but not on 2 different machines. I'm having it between projects on the same machine and have done the following:
To start off, this project has evolved from Atlas, to AJAX beta through RC1 and RC2 to the full release version. The problem only happens when I click on the text box associated with the calendar and there is already a date in the textbox. When it does this it tries to parse the date but the Date class object in the JS code from the axd file doesn't have a parseLocale method, instead it is named localeParse.
So far, I have tested the AjaxControlToolkit project which works just fine. I created my own web project and mirrored the references and includes from my broken project even using the current web config from my other project and the test page works just fine in the new project. If I put a breakpoint on the line of code that breaks:
value = Date.parseLocale(text, this.get_format());
I can see the Date object is different in the 2 projects. The line of code above is from the _parseTextValue : function(text) function in the Calendar control axd Script Resource. When I look at the axd include in the script explorer that has the 2 different Date parseLocale/localeParse methods, the files are obviously different. The thing I don't get is where the old version is coming from. I have removed all of the old AJAX/Atlas code from my machine. The only version of the AJAX code in the C:\Windows\assembly folder are the 1.0.61025.0 versions.
The one difference I had a coworker point out to me was the fact my test project and the AjaxControlToolkit project were both running from the ASP NET Development server. I'm guessing my local IIS instance may be caching the old AJAX code somewhere but that's just a guess. Any input on this would be greatly appreciated.
UNLESS someone like you cares a whole awful lot, nothing is going to get better. It's not!