I'd sort of given up on this at the time and just lived with the erratic
behaviour, but since you asked....

Further notes:
 Tried on a seperate box running Dapper: Same issues (so not the USB port).

 Upgraded seperate box to Edgy: Bug not present. (Fixed!)

 Tried on another seperate box that is running Feisty: Bug not present.

When I run gphoto2 -L under Dapper and it's "working" I get (something
like) the following:

There are no files in folder '/'.
There are no files in folder '/store_00000001'.
There are no files in folder '/store_00000001/DCIM'.
There are 4 files in folder '/store_00000001/DCIM/100CANON':
#1     IMG_3160.JPG                 3538 KB 3504x2336 image/jpeg
#2     IMG_3161.JPG                 3778 KB 3504x2336 image/jpeg
#3     IMG_3162.JPG                 3943 KB 3504x2336 image/jpeg
#4     IMG_3163.JPG                 4052 KB 3504x2336 image/jpeg

When it fails, it only gives:

There are no files in folder '/'.
There are no files in folder '/store_00000001'.

I'm guessing it's either a timing bug, or (IMO much less likely)
something related to the packet size when using the USB PTP protocol.

Notes:
 Ignore the raw mode stuff in the subject. This happens with only jpeg files on 
the device as well.
 gphoto2 -L seems to either work or not work (depending on what I have no idea) 
whereas something like gthumb doesn't work then works once or twice, then stops 
working again.

-- 
Problems caused by raw mode files on target device
https://bugs.launchpad.net/bugs/42506
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