Hi Jaime,
In my experience many of the focus problems people have is usually down to user error. However, there is a chance that your lenses is front or back focussing, and maybe even both. If this is the case it will need a trip to Canon to have calibrated. It isn't a fault in either lens or camera as such, but just one of those anomalies that happen sometimes. The best way to have the lens calibrated is to send it with the camera body to Canon or some other centre that Canon recommend. I think they charge around 60 quid a lens to have this done.
Just to add that when I had my 5d and 24-105 the lens was pin sharp. When I upgraded to the MKII and kept the same lens I had some issues with focus. I always shoot raw and had to review my methods of sharpening images both in ACR and in Photoshop. Let me explain: I do not have any input sharpening (capture sharpening) set in-camera, but I do add some in ACR depending on the image. Sharpening to a minor degree at this stage is essential. It isn't destructive, but needs to be done quite gently. This is usually enough to give me a decent image when imported to PS. I then resize the image to a manageable level (around 49 or 50 MB and do my stuff on it. I save a tiff as my master file and then make a jpeg for posting to the web. I sharpen for these jpegs using LAB Colour and the Lightness channel as 10 times out of 10 the colour channels don't need any sharpening. I return to RGB after I have done this. For prints, I will take a copy from the master file and use the same method of sharpening. This is called Output sharpening. There are a few charts that you can download to check out your lens with before you send it away for calibrating. I use this one here that can be downloaded.
http://www.scribd.com/doc/266756/Cam...cus-Test-Chart
If the lens is under warranty maybe Canon will do it free of charge. Give customer services a ring and tell them of your fears.