I wasn't sure if anyone else was having this problem but I was having trouble with my custom colored SMS bubbles after the update to 4.1 and LimeRa1n JB. I found out what the problem was: The sms bubble pngs used to be named Balloon_1@2x.png and Balloon_2@2x.png. It seems that the update to 4.1 changed them to Balloon_1@2x~iphone.png and Balloon_2@2x~iphone.png. All you have to do to fix it is rename the png files in Winterboard and you're good to go. Just thought I would share this information for anyone who was having the same problems I was.