This also brings up an important point with Web analytics tools. I think it is really important to use more than one tool. It will allow you to double check the information from each tools. Since you are using two different tools, you have to be aware that they will count the information differently but it will tell you if one tool is off the mark.
This is an excellent point Malin -- using more than tool -- and it's something I've raised myself in another post.
I agree that using 2 tools can be a great way to "audit" the accuracy of the data. If you're using a JavaScript page-tagging solution, consider complimenting that with a log file tool such as AWStats.
You should expect to find that the numbers don't match exactly across all tools, up to a certain point. If the discrepancy between both tools is high, this should tell you there's a problem somewhere with the way you've set up your data collection -- maybe you haven't configured the tool properly, etc.
Yann