I moved to Ubuntu 12.10 (using xfce) so 12.04 is no longer applicable to me!
AFAIK the boinc from the berkeley website is not oriented toward
running as user 'boinc' so there might be issues transitioning
from the Ubuntu release version to the berkeley version.

On a recent reboot I found my nvidia 560 TI  unrecognized by boinc.  Powered
down,  reseated the card and its power lines and on reboot it was recognized.

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https://bugs.launchpad.net/bugs/1077316

Title:
  BOINC - no usable GPU found (again)

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