Is it some live version maybe?
Using Wikipedia as a source, it seems like "Colours" was re-recorded three years after it was released for inclusion on Donovan's Greatest Hits. The reason stated seems to be that Epic Records "either unable or unwilling to secure the rights to the original recording" of "Colours". This does seem to hold some truth, as Donovan released the original version of "Colours" on Pye Records in mid-1965, and at the end of the year signed with Epic Records, sparking a contract dispute with Pye.
In addition, this re-recording seems to be the version used in The Rules Of Attraction.