Here are generals that I could find whose promotions were not confirmed:
MAJOR GENERAL
John M. Schofield, appointed 11/29/62, expired 3/3/63, reappointed and confirmed 5/12/63 (backdated to 11/29/62)
John Newton, appointed 3/30/63, expired 3/23/64, never reappointed
BRIGADIER GENERAL
Gabriel R. Paul, appointed 9/5/62, expired 3/4/63, reappointed 4/18/63
Francis L. Vinton, appointed 9/19/62, expired 3/4/63, reappointed 3/13/63, resigned 5/5/63
Henry H. Sibley, appointed 9/29/62, expired 3/4/63, reappointed 3/28/64 (backdated to 3/20/63)
John M. Thayer, appointed 10/4/62, expired 3/4/63, reappointed 4/9/63 (backdated to 3/13/63)
Charles T. Campbell, appointed 11/29/62, expired 3/4/63, reappointed 3/16/63 (backdated to 3/13/63)
Joshua T. Owen, appointed 12/31/62 (backdated to 11/29/62), expired 3/4/63, reappointed 4/9/63 (backdated to 3/30/63)
Robert C. Buchanan, appointed 11/29/62, expired 3/4/63
James H. Ledlie, appointed 11/29/62, expired 1/22/63, reappointed 10/7/63
Wladimir B. Krzyzanowski, appointed 11/29/62, expired 3/9/63
James A. Hardie, appointed 11/29/62, expired 1/22/63
Isham N. Haynie, appointed 11/29/62, expired 1/22/63
Frederick S. Stumbaugh, appointed 11/29/62, expired 1/20/63
David Stuart, appointed 11/29/62, expired 3/4/63
John B.S. Todd, appointed 11/29/62, expired 3/9/63
Thomas G. Stevenson, appointed 12/24/62, expired 3/4/63, reappointed 4/9/63 (backdated to 3/14/63)
Edward Ferrero, appointed 9/10/62, expired 3/4/63, reappointed 5/6/63, revoked 7/21/64
Alexander Chambers, appointed 8/11/63, expired 4/6/64
Gustavus A. DeRussy, appointed 5/23/64, expired 7/4/64, reappointed 7/16/64
Powell Clayton, appointed 8/1/64, expired 3/2/65
Joseph Bailey, appointed 11/10/64, expired 3/4/65, reappointed 4/16/65, resigned before being confirmed
Additionally, there were a number of generals who served who were never confirmed at all. Probably the most famous were Charles C. Gilbert and Orlando Poe but also included Elon Farnsworth, Stephen H. Weed, and Nelson G. Williams.
Ryan