Wonderful script, but for a while I've been thinking there's a bug, and now I'm (reasonably) sure.
I have just finished a run, purchased two skills (stringozzi and tolerance of the kitchen), forced a mafia session refresh, then run the snapshot script. This snapshot was generated:
http://bumcheekcity.com/kol/profile.php?u=Illarion&oldid=71199-bumcheekcity
It correctly lists the generation time as "Generated on 25th November 2011 (3:11 PM) GMT".
The two skills mentioned are not shown (as in, are white, not yellow). Furthermore, Master of the Surprising Fist, which I permed at the end of my last run, is white. Interestingly however, the Good Will Punching and Mixed Martial Arts trophies - both of which I purchased at roughly the same time as Tolerance and Stringozzi, ARE correctly shown in green.
I have tried loading my profile in a different browser (Chrome) than normal (Firefox), and doing a forced refresh in Firefox, and the skills are still not shown - so I don't think it's a caching issue, unless it's at my ISP.
Basically, it seems like the snapshot script only "notices" some changes a while after they occur. I haven't yet been able to pin down what triggers the change - possibly ascending? Possibly restarting Mafia? This seems to occur with skills but not trophies. Anecdotally, I seem to remember issues with familiars and their tourguide/100% status, but I put that down to the script perhaps checking something that only updates after ascension, so didn't worry about it. As a data point, my just completed run was a 100% Hound Dog - the Hound Dog is showing "standard green", ie "you have this familiar but have not done a 100% or Tour Guide run". My PREVIOUS run was a 100% Scarecrow - and the scarecrow is still showing white!
EDIT: For science, I restarted Mafia and ran a new snapshot:
http://bumcheekcity.com/kol/profile.php?u=Illarion&oldid=71201-bumcheekcity
Doesn't seem to have fixed anything.