Don't know if you ever found square liners, but partyworks.com has something called mini loaf liners. When I saw them- it made me think of reading this thread! HTH!

Just wanted to let everyone know I finally found square cupcake papers at Sweet Celebrations (Maid of Scandanavia) www.sweetc.com
They are not in their catalog but they do have a large amount of stock of them 500 liners for about $10.00

Thanks everyone,
Lori V.