Alldata posted TSB AU003-06 for 2006 4Runners (before a certain serial #) relating to abnormal popping noises on FM radio stations. This only affects SR5's and SE's with either the base radio system (without the CD changer) or with the navigation system. The solution is to replace the radio head unit.
http://www.alldata.com/tsb/Toyota/1155020400000_1155625200000_AU003-06/index.html
http://www.alldata.com/tsb/Toyota/1155020400000_1155625200000_AU003-06/index.html