I am not sure what the clock issue was, but DMA was re-enabled on UART 3 via a subsequent patch that also increased the UART DMA RX buffer size. Below is the commit.
commit 191aff8468999abc730ffe4ee0b99fc6afd6a091
Author: Zhang Jiejing <jiejing.zhang@freescale.com>
Date: Fri Apr 1 10:33:26 2011 +0800
ENGR00140702-2 MX5: UART: enable UART3 DMA transfer
- enable DMA transfer of UART3
- enlarge DMA receive buffer size.
Signed-off-by: Zhang Jiejing <jiejing.zhang@freescale.com>
diff --git a/arch/arm/mach-mx5/serial.h b/arch/arm/mach-mx5/serial.h
index 9fbb0b3..6ed55da 100644
--- a/arch/arm/mach-mx5/serial.h
+++ b/arch/arm/mach-mx5/serial.h
@@ -51,8 +51,8 @@
#define UART2_UFCR_TXTL 16
/* UART 3 configuration */
#define UART3_UCR4_CTSTL 16
-#define UART3_DMA_ENABLE 0
-#define UART3_DMA_RXBUFSIZE 1024
+#define UART3_DMA_ENABLE 1
+#define UART3_DMA_RXBUFSIZE 2048
#define UART3_UFCR_RXTL 16
#define UART3_UFCR_TXTL 16
/* UART 4 configuration */