At the risk of repeating what appears to be a very common complaint, I think I have a substantial variation on this bug.
The application won\'t install from Eclipse
This is fixed now. Should someone find themselves with the same unique project setup and bug the solution may be of some value.
The problem stemmed from the configuration of our resource directories in the POM of our test project (the project containing our unit tests). They were pointing to the resource directories of the project being tested. This set up should work so I'm going to guess that it's a bug in the Maven Android plugin that causes the resources to remain unsigned.
So the solution was to remove the references to external resource directories (I can't say why it was done that way initially but removing them appears to have no ill effects) and configure the resource directories in the standard way (taking as an example the POM provided by the maven plugin project archetype with tests).