We have discovered that in order to be able view source for imported classes everyone involved in the project must keep their source at the same path on C:\, and while this is irritating it is required to keep things working smoothly.
Unfortunately setting up a new PC I forgot and created a check out of our repository at a different path which resulted problem described above.
Attempting to fix the issue I deleted the project and the checkout and tried again in the correct place but discovered that though I could retrieve the root node without a problem, EA had cached the version control settings for the nested packages using the old method and nothing I did could cause it to use the correct settings for the entire project. This produced the helpful message:
"The following packages currently have no connection:"
and listed all the child nodes under the root node.
Eventually I resolved it by creating a new VCS configuration under the original name and containing the correct paths so I am creating this post to help other users who might be searching for the error.