I'm also using UART2 for the console. I had the same issue until I modified my board file under arch/arm/mach-mx5/ from...
static void __init mx53_loco_timer_init(void)
{
struct clk *uart_clk;
mx53_clocks_init(32768, 24000000, 0, 0);
uart_clk = clk_get_sys("mxcintuart.0", NULL);
early_console_setup(MX53_BASE_ADDR(UART1_BASE_ADDR), uart_clk);
}
to
static void __init mx53_loco_timer_init(void)
{
struct clk *uart_clk;
mx53_clocks_init(32768, 24000000, 0, 0);
uart_clk = clk_get_sys("mxcintuart.1", NULL);
early_console_setup(MX53_BASE_ADDR(UART2_BASE_ADDR), uart_clk);
}