Disk Utility weirdness: Macintosh HD cannot be repaired but then has no problems?
I have found that when Disk Utility can't repair a disk then it is time for DiskWarrior or another third-party disk repair utility. They can often fix what Disk Utility can not.

However that the issue went away, seemingly by magic, makes Froggard's guess probable.

I would, however, keep an eye on the disk with disk utility. Use the verify function from time to time and if it does not return then it was indeed a transient error that the O/S was able to repair itself.