I also ran into the same problem on LUbuntu 10.04, which increases big file 
transfers times with hours.

Could it be that sftp from Nautilus selects a different cipher for its 
encryption?
Presumably des (the default protocol 1 cipher), judging from the speed drop
compared to plain sftp?

For full details see this posting:
http://ubuntuforums.org/showthread.php?p=12275118#post12275118

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https://bugs.launchpad.net/bugs/250517

Title:
  gvfs performs slowly on bulk sftp transfers

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