A transform shape gotcha Update
You can read the details here
Interestingly I think the scope of the problem was bigger than we originally thought, certainly bigger that what I blogged about anyway, in that even if you don't have the tranform shape problem (for exmample - if you've created the orchestration on a machine with the hotfix, but then opened it in a machine without it) you can have some issues -
In one case we had a map, where the input was composed of several schemas; as you probably know BizTalk effectively creates a schema that aggregate all the parts into a single schema; to achieve this it had to impot several schemas from our solution, all share the same namespace;
When we tried to build the project with the map, we received errors saying a certain element type could not be found, the cause was that BizTalk was looking for it in the wrong schema, as it had several schemas imported into the same namespace, it chose the wonrg one and could not find the type definition.
Once we've installed the fix, and with no other changes, the map compiled all right.