I've encountered the same problem for years now, working in Visual Studio 2008. And I've tried every "solution" on StackOverflow and dozens of blogs, just like I'm sure all of you have. And sometimes they work, and sometimes they don't, just like I'm sure all of you have encountered. And apparently it's still an issue in VS2010 and VS2012.
So finally, a couple of months ago, I decided enough was enough, and over a few weeks I built a tool called "Redesigner" that generates .designer files. It's open-source under the BSD license, with the source code available on SourceForge — free to use, free to steal, free to do anything you please with. And it does what Visual Studio fails to do so often, which is generate .designer files quickly and reliably.
It's a stand-alone command-line tool that parses .aspx and .ascx files, performs all the necessary reflection magic, and spits out correct .designer files. It does all the parsing and reflection itself to avoid relying on existing code, which we all know too well is broken. It's written in C# against .NET 3.5, but it makes pains to avoid using even System.Web for anything other than type declarations, and it doesn't use or rely on Visual Studio at all.
Redesigner can generate new .designer files; and it offers a --verbose option so that when things go wrong, you get far better error messages than "Exception of type System.Exception was thrown." And there's a --verify option that can be used to tell you when your existing .designer files are broken — missing controls, bad property declarations, unreadable by Visual Studio, or otherwise just plain borked.
We've been using it at my workplace to get us out of jams for the better part of the last month now, and while Redesigner is still a beta, it's getting far enough along that it's worth sharing its existence with the public. I soon intend to create a Visual Studio plugin for it so you can simply right-click to verify or regenerate designer files the way you always wished you could. But in the interim, the command-line usage is pretty easy and will save you a lot of headaches.
Anyway, go download a copy of Redesigner now and stop pulling out your hair. You won't always need it, but when you do, you'll be glad you have it!
https://sourceforge.net/projects/redesigner/