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Are you trying to download an accession that is for a chromosome? Can you include an example?
for example: http://www.ncbi.nlm.nih.gov/nuccore/BA000007.2
The last line of the downloaded genbank seqeunce file is "ORIGIN", but the complete genbank file should have sequences behind it.
The genbank format: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html. It mentioned that "The ORIGIN may be left blank". I am wondering if I can get a "full" genbank file with the ORIGIN's have the actual sequences.
Under "Customize view" to the top right, under "Display options" click on "Show Sequence". Then you will get full sequence.
That helps! Thank you!