I have recently came from using selenium-webdriver where all the tests ran fine but with capybara webkit i have this issue so it must be specific to capybara-webkit.
I found this by outputting page.html into the console.
Can you put together a test to reproduce this?
I'm closing this issue due to the long time of inactivity. Please re-open it if you're still experiencing these issues using the latest version of capybara-webkit.