Christopher - I assume that you have updated the versions in both those
partitions to date, so that in theory they should be the same (except
for any customizations you may have made).

If so, it would be interesting to run apt-show-versions in each
partition (you may have to install that program), saving the output of
each in a file, then do a diff between the two files. That may show some
differences between the packages in each partition.

Just a thought!

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visual corruption affecting several panel applets
https://bugs.launchpad.net/bugs/439448
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