I think the problem is due to the way fees are calculated now due to network congestion. I'm not sure why the notice disappeared. I would recommend you backup your wallet, and upgrade to 0.12.1.
Just upgrade to Bitcoin Core 0.12.1. The upgrade will not mess with your wallet, and you will not need to redownload the blockchain. To be safe, you should backup the wallet file to a safe location. Just go to File > Backup Wallet and save the file to a safe place.
Thanks for the quick replies! I have one more question: I assume that the "File > Backup Wallet" instructions are for Windows? If so, can you tell me how do I do it on a Mac? I just bought it, and can figure it out.
Also, how exactly do I upgrade to the new version on a Mac?
Thank you!