fixed this by adding
"libata.force=noncq" to the grub config. i totally forgot that i did that with 
my first install. the laptop now boots in 7 seconds from the moment of the 
ubuntu password boot screen, to the desktop. before that it took way over one 
minute.
it works every time!

i also use the v3.12-saucy kernel, that fixed the haswell cpu throttling
to 800mhz.

stock 13.10 is not usable on the vaio pro. let's hope 14.04. i will stick with 
this stable release/system.
here's a nice list, what needed to be done to get 13.10 working on the vaio 
pro: http://steffankarger.nl/2013/12/10/ubuntu-13-10-on-the-sony-vaio-pro-13/

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https://bugs.launchpad.net/bugs/1265381

Title:
  [Sony VAIO SVP1321C5E] luks/lvm encrypted 13.10 installation doesn't
  reliably boot

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