Okay, story time.
On my mid-2009 macbook pro, I decided to replace my Windows bootcamp with Ubuntu. Removing bootcamp went okay. After that, I installed a program called rEFIt, which lets you choose what you want to boot to every time you boot up, and manage your partitions too. I installed linux, but after running into some driver problems, I decided to uninstall. I uninstalled it, removed the partition, and removed rEFIt, too. Everything appeared to be normal. I noticed that when I pressed Get Info on my Macintosh HD, it said the total size was 90 GB, when the real size of the partition is 120 GB. I thought that was a little odd, but didn't think much of it at the time. A few weeks later, I was trying to create a new partition with Disk Utility, and it said I had to repair the disk. So I booted into the recovery partition and clicked repair disk. It then immediatly said "Alert: This disk does not contain a efi system partition. If you want to start up your computer with this disk, back up your data and repartition this disk.". The funny thing is, I could still start up normally. I then decided to look at diskutil and see if anything in there helped. Here's what I got:
#: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *160.0 GB disk0
1: Apple_HFS Macintosh HD 129.2 GB disk0s1
2: Apple_HFS Recovery HD 650.0 MB disk0s2
3: EFI 209.7 MB disk0s3
Okay, everything looks normal here. I am totally stumped on what to do, since the EFI appears to be there and there aren't any other partitions. Any advice?