Did you get UART2 & 3 working? How?
Lily is correct. The mx51 iomux header file must be updated to correct the UART2 pin settings...
Please remove daisy setting for TX PINs. For example:
#define MX53_PAD_EMI_D27__UART2_RXD IOMUX_PAD(0x490, 0x148, 2, 0x888, 1, MX53_UART_PAD_CTRL)
#define MX53_PAD_EMI_D26__UART2_TXD IOMUX_PAD(0x48C, 0x144, 0, 0, 0, MX53_UART_PAD_CTRL)
#define MX53_PAD_EMI_D24__UART3_TXD IOMUX_PAD(0x484, 0x13C, 2, 0x888, 0, MX53_UART_PAD_CTRL)
#define MX53_PAD_EMI_D25__UART3_RXD IOMUX_PAD(0x488, 0x140, 0, 0, 0, MX53_UART_PAD_CTRL)
Maybe cased by DMA, please change arch/arm/mach-mx5/serial.h diable the DMA of these ports.
By the way, what's you version ?