Hello Blue@controller,
The first thing you can try is to update your plug-in. If you go to the following link you can update to 2013.3 for Maya 2011.
http://usa.autodesk.com/adsk/servlet/pc/item?siteID=123112&id=10775855#Usually those warnings are not something that should break your rig, but have you tried to create a new bind pose for your character? As well, what happens if you export your character and then re-import it into Maya. If the import into Maya is succesful, then the plug-in is working correctly (even if there is a warning). The fact that it won't import into Unity is a problem with the importer the Unity uses, which is something that Autodesk does not support. I suggest you find a forum where the Unity developers can offer some assistance because these particular forums only address problems concerning the Max and Maya plug-ins and the way the work with Autodesk products.
Like I mentioned though, update your plug-in to 2013.3 first, and do the export - import test. If you import the file back into Maya and there is still a problem, write back here and if possible, attach the rig, I will get on it.
Regards,
Carlos