hi paul,
that's a bug (./configure --enable-gsl=no doesn't work). you need gsl-dev. (which is the GNU Scientific Library)
about libquicktime. it does seem to have quite some bugs indeed, especially when you try to stress it (open/close a lot of files).
next to yves' theora in pidip there will be a raw uncompressed video format soon in pdp/pf. i made it compatible with block devices so you can use raw partitions for maximum efficiency.
tom