The trouble with running scans from another OS is the scanners can't check live/active nasties and they can get permission issues with files/folders.
Security permissions only apply to OS settings, if you boot from BartPE or MiniXP they flout security permissions so stuff like SVI and system registry files can be accessed.
As for can't check live active nasties that may well be true, but a good anti-virus program with heuristic capabilities or signature based should prove quite effective (except for AVG).
Heuristic results should however be taken at face value I've had instances where genuine programs, applications even my own work have been flagged up by AVG even though I know them to be 100% clean.
If you have a persistent nasty on your Windows drive then a boot CD with Windows OS would prove useful i.e. inspecting registry entries for auto starts with Sysinternals Autoruns, checking file creation time stamp to confirm whether a program file or driver file had been created at the time of infection, or performing a manual system restore with SVI snapshots. (etc...)