It's not just Revit 2012, it's all Revit versions that have this stupid meaningless message that makes us users waste countless hours trying to get it to work!!
I had a similar issue on a current project and found that sometimes if I verified that elements were perpendicular to each other (where obviously 90 deg was needed) and making sure that elements where in alignment along a run, especially where you transition between horizontal and vertical, this solved the problem. That said I still have two systems that show that message no matter what I try.
I also have one message where an air terminal is ducted to an AHU and despite the connectors being set correctly the system can't calculate anything as it reckons the connectors are all set the same, i.e preset or calculated. As I mentioned to Martin S in a previous post - I think that by making the systems "Simpler" for users to specify that a pipe/duct can be any type of system rather than using connectors to drive it, this leads to more hassle for us, especially if you are not regimented in setting up your system prior connecting the dots with pipes/ducts.
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