When I installed Trisquel in my notebook, I just selected the text-mode
installation, choosed the default LVM/LUKS partitioning scheme and everything
went fine.
I don't know what's happening, but I /always/ had problems with Ubiquity when
trying to do something different. I think it's some KISS curse on me ;P
If the partitioning scheme is complete, try to boot the Live CD again and
install Trisquel, hoping it will know what to do... I would suggest the
text-mode installer, which have the LVM/LUKS option. Maybe you will only need
to give the needed informations to the installer.