A simulator that doesn't produce accurate results sends you wasting time chasing problems that exist only in simulations, and does not provide assurance that your design works. There is really no substitute for prototyping your design and testing it there - I am of the opinion that proteus is a waste of time.
We often get people posting about a problem that turns up in a proteus simulation which, when running on the actual hardware, doesn't occur - the simulation does not reflect reality. Arduino Proteus library files to be assigned to Proteus LIBRARY C:Program FilesLabcenter ElectronicsProteus X ProfessionalLIBRARY. As far as I am aware, basically anything that claims to simulate the behavior of a microcontroller (ie, including what the code does) is garbage. I have not a clue if this is relevant here, and this may be a total red herring, but whenever I have a program where I have to change things inside it's installation folder, I install it outside of program files to rule out this madness. Particularly on Vista, where this was buggier, situations that should be impossible can occur.
Windows UAC File and Registry Virtualization can, depending on settings, cause wacky behavior with files in protected locations (like program files), where depending on what privilege level a process is running as, different files or file contents will be seen (ie, a process run as admin will see different files, or different file contents than a process running without admin privileges).
