You made some comments about how only one partition was affected and so
it shouldn't have had to touch the partition table. While this is great
in theory, unfortunately it isn't how the kernel works. :-( If you
modify the properties of any partition on the disk (I don't mean the
data on the partition here - I mean things like the partition type, or
adding or deleting a partition), then you have to tell the kernel to
reread the whole partition table, which it will only consent to do if
*none* of the partitions on the disk are "busy". Loop-mounting the
installer from a file on one of the partitions on the same disk counts
as that partition being busy. This is why I do not advise using the
installer this way - it's very difficult.

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Jaunty: installing to existing JFS partition from existing Ubuntu installation 
without burning CD fails due to HD partitioning
https://bugs.launchpad.net/bugs/313452
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