I did check file permissions.
The upgrade document has a sentence saying to upload files and directories from the unzipped file except for a couple of directories and one php file. Under that sentence is Upload These: followed by a list of files and directories.
There are some files and directories that are not lised under Upload These - like templates/compile and some files in the styles directory. The instructions don't include those files in the list that should be uploaded and they also are not in the list to not be uploaded. Should those be uploaded?