After upgrading to a new instance of BizTalk Server (2006 to 2010), strange behaviour was seen with a customised Voucher load. All of the records were imported into 3e, but certain internal 3e Object Code operations were not being performed to amend the imported data. This only happened when the imported flat file was greater than a particular size (32,218 Bytes in this case).
Following advice from this article, I changed the value of the Large Message Size in the BizTalk Group Settings from 100KB to 315KB.
This solves the problem. It seems message fragmentation caused by an insufficient message size threw errors which eventually led to the Process in 3e not executing methods further downstream.
See this msdn blog post for further information.
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