In order to download your meter data in the same units in which you entered, select "Custom Download" from the bottom of your MyPortfolio tab:
Then select the properties, meter entries, and timeframe.
Note: The limit for this download is 50,000 rows. Therefore you may have to break up your download into smaller sections.
If you download the data in a Custom Report, the units will be in kBtu regardless of how they were entered into Portfolio Manager.