The best way to explain this is to show you the attached screenshot. Basically, the corners aren't transparent like they used to be - there is now black around them. You can see the screenshot here, since I couldn't figure out how to upload/attach something to this post:
https://www.evernote.com/shard/s19/sh/ebda03b2-eff5-4d2c-ba9d-e2558279302d/d8363b1b258be3636642f04dfe6752c8
I am running:
OS X 10.10.1
Alfred v2.6 (374)
This always happens, nothing gets rid of it or changes it.