The update to EGit v2.3 did solve some other annoyances I had been seeing. But looking at the repo using Git Extensions I realised I had a copy of the linked file sitting in the repo directory - essentially duplicating the file in the project (i.e. there was a copy of the asm file in the project dir BUT the project settings was telling the project to also go link to the same asm file at another location).
I figured this might be snarling up the .project file somehow so I removed the link from the project, rebuilt and sure enough the file from the project dir was added to the project. The subsequent commit and push ran OK!