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I too experience this problem of Batch register to the point now I am thinking this feature just does not work.
I am familiar with this module before GIJOE updated it and the Batch register worked correctly then.
Like you I have tried every permetation I can think of and still receive 'Invalid Directory' warning.
So your not alone, and also on other XOOPS web sites others are asking, experiencing the exact same problem world wide.
This is a good updated module by GIJOE. I wish the batch register would operate correctly, as I too update on batch.
Cheers