Someone can correct me but my quick check shows no compilation album on those years Brian releases a solo for quite a few years.
The exceptions are 2002 with the Classics chosen by Brian, and 2005 with the Platimum collection for Summer then Brians album for Christmas. Its almost odd years for the Beach Boys, Evens for Brian.
Beach Boy Compilations
Greatest Hits Vol. 1
(1999)
Greatest Hits Vol. 2
(1999)
Greatest Hits Vol. 3
The Very Best of the Beach Boys (2001)
Classics Selected by
Brian Wilson
(2002)
Sounds of Summer
(2003)
The Platinum Collection
Sounds of Summer Edition
(2005)
The Warmth of the Sun
(2007)
Brian Albums
Imagination (June 16, 1998)
Live at the Roxy Theatre (June, 2000)
Pet Sounds Live (June 11, 2002)
Gettin' in Over My Head (June 22, 2004)
Smile (September 28, 2004)
What I Really Want for Christmas (October 18, 2005)
That Lucky Old Sun (September 2, 2008)
Brian Wilson Reimagines Gershwin (August 17, 2010)