I was seeing file access errors (not permissions but actual failing to read the files), so I am reasonably sure the drive was failing.
As an update, I have run the disk utility to fix permissions again, and although the problems are not gone entirely, they are much less frequent.
I also found...
A few weeks ago my Macbook Pro hard drive started to fail and I replaced it. Since then I have had a handful of issues that seem to randomly occur after each boot.
For example, one time after cold boot, the grey screen (apple and gear) will hang forever. If I power cycle, the next boot might...