[noelwelsh]

This is relevant: http://news.ycombinator.com/item?id=4997127

The answer is: it depends. How much data did you collect? How big was the difference you observed?

Javascript is less reliable than server-side tracking. There are lots of issues. Some people have Javascript turned off, though normally this is a small proportion. If people navigate away before the testing harness is loaded you can lose data. If you're testing elements that navigate away from the current page you can lose data if the harness is not implemented correctly (the browser will cancel pending requests when you navigate away).

I can't say what went wrong in your case but there is the potential for lots to go wrong.