I don't think the OP is asking for help removing DRM at all - he or she writes 'I've got the .mobi file DRM-free'
So far as I can tell she or he wants help in converting a DRM free mobi file to run on the iPad. The only help I can offer is that there have been changes in iBooks which have messed up the ADE ePub to iBooks ePub conversions I do from time to time. So it might be the changes in iBooks which are causing the problem.
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