These issues often baffle me as well, usually at some hair-tearing 'why has it done that?' moment. FWIW, I think that there are a number of factors that contribute to the general mess which is Windows permissions.
Firstly, the users/permissions concept is just not very well implemented in Windows, and lacks the strict logic that you find in, for example, Linux. Microsoft has tried to find a balance between users (such as home or single users like yourself) who have no need for the facility and want to be spared the complication, and corporate users who need to maintain strict and secure controls. Because the latter requirement demands that the OS runs a permissions system at all times, Microsoft has from XP on simplified the user interface for home users by (paradoxically) adding extra layers of complexity; when something happens under the hood that the user does not understand, the only way to resolve the problem is to get into the gory detail, going through layers of confusing menus to do something that in Linux can be achieved with a one line console command. In XP Home, some of the functionality needed to resolve problems was actually unavailable to users.
Second, the way in which permissions are inherited in Windows/NTFS can produce unexpected and counter-intuitive results; problems in this area can then only be resolved by doing battle with the menus as aforesaid.
Third, there was a change from XP to Vista (and now Win7); in XP, accounts with administrative privileges were always run 'as administrator' (aka 'elevated'), while from Vista on they run by default as normal accounts, and individual programs have to be explicitly run elevated to gain administrator privileges. It is apparent, not least from posts to this forum, that many former XP users are unaware of this change and its implications.
Fourth there are some (actually rather a lot of) files in Vista and Win7 which are owned by a special system account to which the user, administrator or not, has no access. To my way of thinking, this is security gone mad, but there it is.
My guess is that your system has been bitten by one or more of these issues. Mine have, many times.