Far as I know, Woody Guthrie learned it from an African American shoeshine boy in Okemah, Oklahoma. Story's in John & Alan Lomax Folk Song: USA / Best-Loved American Folk Songs. So it appears to be an actual folk song, no matter who's attached a copyright.
"I would like to hear anyone else's ideas on where this great tune came from..."
This is my take on it:
TRAIN 45. Often played as an instrumental in bluegrass, this song is a version of “Reuben’s Train” popular in various forms since 1898. Fiddlin’ John Carson recorded it for OKeh in 1924 as “I’m 900 Miles from My Home”, Norman Gayle for Champion in 1927 as “Train No. 45” (crediting Whitter), George Banman Grayson & Henry Whitter for Victor in 1927 as “(Old) Train Forty-Five”--for Gennett in 1927 as “Train No. 45”--for Bluebird in 1927 as “Train 45” (County Records reissued their version for the 1999 album The Recordings of Grayson & Whitter, and Document Records reissued it for the 2000 Grayson & Whitter album The Complete Recorded Works in Chronological Order, Volume I: 1927–1928), Fleming and Townsend for Bluebird in 1927, David Foley for Challenge in 1928 as “Train Number 45”, Riley Puckett for Columbia in 1929 as “Nine Hundred Miles from Home, Emry Arthur for Paramount in 1931 under the title “Reuben oh Reuben”, the Carolina Ramblers String Band for Perfect/Banner in 1932 as “Reuben’s Train”, Wade Mainer, Zeke Morris & Steve Ledford for Bluebird in 1937 (crediting Zeke Morris) under the title “Riding on That Train Forty Five” (Rounder Records reissued it for the 1998 compilation album Train 45: Railroad Songs of the Early 1900s), Zeke Morris for Victor in 1941 as “Riding Train No. 45”, Wade Mainer & the Sons of the Mountaineers for Bluebird in 1941 under the title “Old Reuben”, and Woody Guthrie for Moses Asch in 1944. Sometimes, versions of this song appear under the titles “500 (or 900) Miles from my Home”. Bill Monroe & His Blue Grass Boys released this version on a 45 rpm single for Decca Records in January 1968 (MCA Records reissued the song for the 1983 Bill Monroe album Bluegrass Collection, Volume IV, and Bear Family reissued it for the 1991 Bill Monroe box set Bluegrass: 1959-1969). He recorded it again at Bean Blossom in 1979 (MCA Records released it in 1980 under the title Bean Blossom 79 and Bear Family Records reissued it for the 1994 Bill Monroe album Bluegrass 1970-79). Among others, Sonny Osborne released the song (as an instrumental) for his 195? Gateway album Five String Hi Fi, the Laurel River Valley Boys for their 1958 Judson Records album Music for Moonshiners, the Stanley Brothers (instrumental) for their 1958 King Records album The Stanley Brothers and the Clinch Mountain Boys (Gusto’s Hollywood label reissued it for the 1997 Stanley Brothers album 16 Greatest Hits; King Records reissued it for the 1997 album The Stanley Brothers & the Clinch Mountain Boys; Westside for the 1999 Stanley Brothers album 1958-1961: Ridin’ That Midnight Train; and King Records reissued it for the 2000 Stanley Brothers album Complete Starday and King Instrumentals, for the 2002 Stanley Brothers album All Time Greatest Hits, and for the 2003 Stanley Brothers box set The King Years: 1961-1965), Country Gentlemen (instrumental) for their 1961 Folkways Records album Folk Songs & Bluegrass (Smithsonian Folkways reissued that album in 1991), the Osborne Brothers for their 1962 MGM Records album Bluegrass Instrumentals, Jimmy Martin (instrumental) for his 1962 Decca Records album Country Music Time (Bear Family reissued it for the 1994 box set Jimmy Martin), the Potomac Valley Boys for their 1970 GHP Records album Bluegrass from Virginia, J. D. Crowe & the Kentucky Mountain Boys (instrumental) for their 1973 King Bluegrass Records album Bluegrass Holiday (a reissue of their 1968 Lemco album of the same title), Ralph Stanley (instrumental) for his 1974 Rebel album A Man and His Music (Rebel reissued it for the 1995 Ralph Stanley album Classic Bluegrass and for the 1995 Ralph Stanley box set 1971-1973), Ola Belle Reed under the title “Ruben” in 1975 for Heritage Records, J. D. Crowe & the New South (instrumental) for their 1976 Towa Records album Live in Japan, Mac Wiseman for his 1990 CMH Records album Grassroots To Bluegrass, Benton Flippen (instrumental) for his 1994 Rounder Select album Old Time, New Times, the New Lost City Ramblers for their 1994 Vanguard Records album Old Time Music, Ralph Stanley for his 1996 Rebel Records Grayson & Whitter tribute album Short Life of Trouble, the Kentucky Colonels (instrumental) for their 1997 Hollywood Records album Livin In the Past, Raymond Fairchild (instrumental) for his 1997 Rural Rhythm Records album 31 Banjo Favorites (Volume I), Del McCoury & his Dixie Pals (instrumental) for their 2000 Vivid label album Stricktly Bluegrass Live, Doyle Lawson (instrumental) for his 2004 Crossroads Records album School of Bluegrass, the Stanley Brothers again (recorded in 1956) for their 2004 Columbia Records album An Evening Long Ago: Live 1956, and Tangleweed for their 2005 Squatney label album Just a Spoonful.
900 miles is of course a member of the "Reuben" family. But unlike other related tunes and songs, it's in minor. I usually play it in Gm tuning on the banjo. It's also got a slightly more complex and longer melody.