Comment 44 for bug 62195

Well, the fix to this problem is trivial. Actually there are many possible fixes.

a) make the script note that the conversion was already performed, and not re-convert

b) make a separate script for the conversion and run it on system install or system upgrade but not on package upgrade

c) make a dpkg(debconf) question about this that people using apt/aptitude directly would see and people using graphics would not

....

The non-trivial part about some bugs (both Joe @ home style and advanced user style) is to convince Ubuntu people that a fix is indeed needed.

Since you found such a bug and it gets in your way my only advice is:

Switch to some other distro!
Do it right now, don't hold you breath!!

The Ubuntu people are really stubborn, and if they decided to not fix something they won't.

Oh, and thanks to whoever posted the link for building a kernel package. Building a packaged kernel with autogenerated initramfs makes using UUIDs with custom kernels easy but that apparently does not fix everything.