The most common reason I see that happen are registry cleaners that remove a setting to tell Windows to ignore low space on D. What happens next is the owner runs a cleaner and maybe does more damage.
The issue about permissions is not about "administrator." I'd rather not go too deep into that but an administrator is not God so permissions must be obeyed and if there is a need to change them, we do that since we, as the administrator can do that.
-> Defrag is NOT A TOOL TO BE USED FOR THE ISSUES NOTED SO FAR. STOP! DON'T DO THAT! Defragging a PC with troubles will cause mroe troubles.
With those items out of the way we are boiling this down to the installer issue. Pick over prior discussions from the next link.
https://www.google.com/search?hl=en&as_q=windows+installer+may+not+be+properly+installed+vista
Bob
Now that i've done a system restore point (I had to go into safe mode even to do that), I can't even upgrade my virus protection. It all began with getting a dialgue box constantly telling me "you are running out of disk space on RECOVERY (D). I did the clean up files thing numerous times to no avail. Also, though I am the administrator and have been for 6 yrs. or so, now I get "windows cannot access the specified device, path or file. You may not have appropriate permissions to access the item." Tried to run defrag. Same message. as above. I have tried to click on the "run as administrator" suggestion. I have never set a password as administrator either. Then one more issue, whenever I try to uninstall a program for instance, another message I get is "windows installer may not be properly installed". I have never had these types of issues with this computer. It is a hp pavilion entertainment pc running Windows Vista Home Premium 64bit. Model dv2-1030. I have spent hours trying to figure out what's wrong! ANY help would be greatly appreciated.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic