I just wanted to touch back as I found the real cause of the issue:
1) The LCD screen we are using has different timings than the stock ones provided in the drivers/video/mxc/ldb.c
2) Specifying dev=ldb,1280x800M makes the kernel using the timings from drivers/video/modedb.c and not drivers/video/mxc/ldb.c
The proper bootargs for my device was:
video=mxcfb0:dev=ldb,LDB-WXGA video=mxcfb1:dev=hdmi,1920x1080M@60,if=RGB24,bpp=32 video=mxcfb2:off
fbmem=28M,28M vmalloc=400M androidboot.console=ttymxc0 androidboot.hardware=freescale
The proper changes to the ldb.c file were:
"LDB-WXGA", 60, 1280, 800, 13812,
40, 40,
10, 3,
80, 20,
0,
FB_VMODE_NONINTERLACED,
FB_MODE_IS_DETAILED,