Obvious question would be: Are the aliases still valid after your OS upgrade?
I'm not at my Mac tonight* but upgrading to 22.214.171.124 would be worth your while, I definitely fixed something to do with right-clicking on aliases (the bug manifested itself so that FP accidentally offered you the ability to move the alias you clicked on into whatever the alias pointed to, but I think this might be the same bug that you're seeing.)viewtopic.php?f=3&t=155
Let me know if this doesn't fix your problem!
* I'd love to be "at my Mac" but I'm up the walls with "real" work - something came up today and I'll be busy for the rest of the week. At least!