Why wasn't the iconic Metal Gear Solid theme used in Metal Gear Solid 4? Because, as Gamasutra reports, EGM learned in an interview with series composer Norihiko Hibino that unnamed Russian composers claimed Konami "stole their music."
A video posted on YouTube (viewable here) shows series creator, Hideo Kojima, being presented with a recording of Georgy Sviridov's "Pushkin's Garland," a 1979 classical work which contains a similar-sounding passage. The MGS theme was first heard in the original PlayStation game, circa 1995 1998. It was written by Konami's Tappi "TAPPY" Iwase, and has subsequently been reworked and remixed, most notably by film composer Harry Gregson-Williams, who scored MGS2-4.
Speaking to EGM, Hibino flatly denies that the MGS theme was "stolen," but admits that "Konami was too sensitive about the situation and just decided not to use that music in the game."