This is, believe or not, NOT quicksilver's bug. Not really.
Snow Leopard changed the nature of Services pretty seriously. The
Service's plugin for Quicksilver was written for Tiger. It's not a
bug, it's in need of at least a partial update.
However, I was going to take a look and see if Skype is
applescriptable for you. And realized its very applescriptable, and
wrote a Quicksilver action to send phone numbers to Skype to make a
call.
You can download it here:
http://tr.im/D4J6
Install it to: ~/Library/Application Support/Quicksilver/Actions
Then restart QS.
To use, grab a phone number from your address book (requires the
address book plugin), or type in a phone number in QS text entry mode.
Tab over and type till you see callSkype, hit enter.
This should work. I've got it set to first strip out parenthesis,
dashes, and spaces from the number so you don't need to worry about
that formatting. Then it checks if the first character of the phone
number is a "+" (skype needs phone numbers to be in the format
"+CCC1234567890", where CCC is the country code. If you want to call
outside the US you'll need to make sure you numbers are in that
format. Inside the US they can be formatted for skype, but if they're
not (if there's no "+" at the beginning) the script tacks on a "+1"
for you. If you store your numbers as "1(222)333-4444", that's ok
too. In the case of numbers not starting with "+", the script takes
the last 10 digits of whatever you send it and adds the "+1".
I'll post this in the main board as an action as well. But you can
download it at the link above.