We have a number of popups (generated using Javascript) that are displayed during page navigation.
When we record the webtest, the script doesn't capture all of them.
If there a way around this?
The load tests do no render javascript, but operate solely by recording individiual http requests. So no, there is no way around this.
Investigate the new Visual Studio 2010 Coded UI test for testing the operation of the UI.
I think this is the tool for the job, however I do not have any experience with it.