Oh that's ridiculous!
Sure, Canon will simply turn off the BootFlag, you can do this yourself and save all the trouble time and money of taking your camera to a service centre.
The way to fix this problem is in the following manner.
With a Magic Lantern Bootable Chip intalled in your camera, select firware upgrade, once selected, follow the menu and change it to remove Magic lantern from you camera, then once you have the green text screen move your camera dial to a position other than the bootflag ones mentioned on that screen, example select (Full Auto), then power off you camera, inert your Eye-Fi and it will now work.
You Eye-Fi card will then work fine as the bootflag is no longer on! thats all it is that stops it from functioning.
The Eye-Fi card simply wont handle bootflag being on (nothing more, nothing less), Magic Lantern needs the bootflag on in order to load the firmware, if its a choice between the two I know like me and most of you that you would rather have the magic lantern software as opposed to being able to wireless send your images to another device. I guess its the 100 benefits like video audio image etc as opposed to 1 benefit being wireless.
I hope the Eye-Fi developers rectify this soon with a firmware upgrade otherwise people will start selling their X2's and purchase the other WiFi SD cards that are becoming available on the market, a search on eBay and already there are several brands available.
I think it should be as simple as setting a flag in software.... but Im not a software developer.
Anyhow good luck with it all, better hurry is all I can say as people would want to have both the magic lantern and wifi capable cards.