I concur that Witt's 10th is another posibility. Unless we stumble on some previously unknow document that links those men of the 48th listed as captured in Missouri with one of the units/commanders that we know about, this mystery may never be solved. I know Bryan has copies of what appears to be minutes of the State Military Board that lists the commanders for most of the 40 Series regiments, but I don't think it identifies the comander of the 48th. I think the most likely sources that could help would be either family records or pension applications from one of these men that indicates what commander he served under during Price's Raid.

BEARD, LEWIS - PVT - G - Captured 24 Oct 1864 at Mound City, KS. Died 7 ? 1864 of rubela at Alton, IL
BURNES, ANDREW J. - PVT - F - Captured 24 Oct 1864 at Mound City, KS..
CHRISTWELL, DAVID - PVT - A - Captured 24 Oct 1864 at Mound City, KS. Died 12 Mar 1865 of pneumonia at Alton, IL #1913
JONES, THOMAS S. - PVT - B Captured 24 Oct 1864 at Mound City, KS
PICKENS, DAVID F. - PVT - C - Captured in White Co, AR 14 Aug 1864
PORTER, URIAH - PVT - G - Captured 24 Oct 1864 at Mound City, KS
QUATTLEBAUM, PHILIP - CPL - G - Captured 24 Oct 1864 at Mound City, KS
QUERY, SMILEY P. - PVT - G - Captured 11 Nov 1864 in White Co, AR
WALKER, W.B. - PVT - D - Captured at Pilot Knob, MO 27 Sep 1864