I replaced the shifter boot and then the E-Brake boots and I bought them from Redlinegoods.com and I had a color problem but thats fixed and I thought I'd post the finished pictures. The shifter boot is made out or leather and the original is made out of vinyl, so if and when you think you'd like to do this, there are 8 little clips that hold the shifter boot on the underside of the console, you'll need to take them to a vise and open them up using a screwdriver, or some other leverage type tool ( The new leather is thicker than the Vinyl ) and I didn't want to remove the console, so once it's loose, I put a cardboard box under the back of the console and it will hold it up so you can install the boot, then just lower it back down and screw it back together. 

And I then decided it looked odd only the shifter boot being a different color so I ordered a E-brake boot from the same company. Now the difference here is the original boot has push-snaps to hold it to the carpet on the tunnel, but Redlinegoods.com can't do the snap-clips. So if you want to replace the boot with snaps, I can tell you what you'll need and where to get them, ( it is not a big deal, and they are pretty cheap) But I did mine and this is what the finished product looks like :

 

I think your hand brake boot isn't tucked in properly.

Looks good! Thx for the pictures.

My E-brake boot has a tear in it.  So, i ordered a new one off ebay.  The placement of the snaps was so poor that i just threw it away.  I couldn't stand to look at the wrinkles it created.