Not long time ago I came across this problem while I was trying to update an esxi 5.5 from update1 to update3 Dell servers R630 arrived with preinstalled esxi on a raid1 composed by two SD cards. The attempt to update is made by inserting the CD at the server boot time (in fact in this case, by mounting the iso via the idrac but this doesn't change anything) and initiating the procedure for server upgrade. After you select the volume that contains the installation to upgrade this error occurred:
ESXi upgrade operation failed – Error: permission denied
As if the partition (or one of the partitions) was in read only and can not be changed. I tried to see if there was some bios setting which made the SD cards read only but so was not, the second thing I checked was if, for some strange reason, one of the SD card had the “switch” that was physically blocking the writing but it was not even that. Not having much time to investigate thoroughly I decided to try to make a fresh install and reconfigure the host and in this case the process has been successful.
If anyone had a similar problem and managed to solve in some other way (for example by changing the partition type 0xfb that is reported in the error with some command) please inform through the comments below, I'll update the post!