Dear Richard,
the first thing I would do is to load the batch template into the GUI. Although there are not many things that have changed in first level fMRI, there might be some subtle differences (e.g. toolbox availability, some changed/missing default settings) that might cause additional '<-X' marks or dropped/missing dependencies in your template. SPM12 tries to be clever and update batches if necessary, but it might fail doing that correctly.
If it turns out to be a bug in SPM12 or an incompatibility between SPM8 and SPM12 it would be nice if you could share your batch template and document the changed features on this list.
Best,
Volkmar
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