Hmmm. It is odd, I followed the same steps with a simple table for testing, and do not get an error, even if I don't have my form set to update. It sounds like you have a work-around (manually modify the existing XML), but I hope you don't have too many existing forms that have to be updated.
One thing you could check would be the max version to upgrade in the manifest.xsf file. Save your form as source files, and open manifest.xsf in a text editor. Make a note of the current version number:
<xsf:xDocumentClass trustSetting="automatic" solutionFormatVersion="2.0.0.0" dataFormSolution="yes" solutionVersion="1.0.0.5"
Then, toward the bottom of the file, look to make sure your max version is correct:
<xsf:documentVersionUpgrade>
<xsf:useTransform transform="upgrade.xsl" minVersionToUpgrade="0.0.0.0" maxVersionToUpgrade="1.0.0.5">
</xsf:useTransform>
However, as I mentioned, when I tested locally, even if my template is not set to upgrade, I cannot reproduce this issue....