I am having the same problem too, it doesn't matter whether the project was converted from .NET 2003 or if it is a new one from 2005.
One thing that I have noticed is that if VS 2005 thinks there is an error in parsing the page, then changes to controls are not updated in the designer file. Fixing the HTML problems I think helps, but I am not sure if that's the solution or not.
Another thing I noticed was that the my intellisense wasn't working when this problem occurs as well.
What I did do to get this to work correctly was to fix any HTML problems on the form. Try to close the form and re-open it, if intellisense is working, do a test with a simple text box. If that works you're good to go. If none of these work, go back and see if your HTML code is valid and your front page code is valid and try to close all of your files in your solution, then shut down VS 2005 and re-open it. That seems to have worked for me.
Hope this helps.