What version of calibre are you using. Automated margin removal for conversions to epub have recently been updated twice. If you aren't using a new version update and convert again.
If you have a current version follow lila55's info.
Quote:
Release: 0.7.51 [25 Mar, 2011]
New Features
- Conversion: Detect and remove fake page margins that are specified as a margin on (nearly) every paragraph. This can be turned off via an option under Structure Detection, in case it removes margins that should have been kept.
Release: 0.7.53 [01 Apr, 2011]
New Features
- EPUB Output: Remove any margins specified via an Adobe page template in the input document. This means that the margins specified in calibre are more likely to be the actual margins used.
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