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One possibility:
If you have custom conflict filters developed, make sure they are configured on the machine that is doing the batch reconcile. I also discovered with ours that when ESRI and MM changed (around ArcGIS 9.2?) to requiring code to manually initiate licenses that my custom conflict filters were failing. I needed to make sure the reconcile app was checking out an ArcFM license.
I've seen this behavior also since upgrading to ArcGIS 9.3. I'm not sure that is the cause but it's one clue. Since the upgrade to 9.3 I have a version that is the child of another version, not DEFAULT. It has conflicts when batch reconciled, but reconciles without conflicts when run in ArcMap. The report from my conflict filter shows that the shape length for two features in the version have conflicts and it fixes them by taking the conflict version, but when I check afterwards, the shape length is still slightly different from it's parent which it should have just copied. I know with network features, changing the shape of a connected feature will cause adjacent features to adjust, but then I should be seeing conflicts with those features as well but I'm not. I have not had time to fully analyze this - this is just what I've noticed so far.
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