diff --git a/arch/sh/drivers/pci/ops-sh7786.c b/arch/sh/drivers/pci/ops-sh7786.c
index 48f594b9582b..79a5ddae733d 100644
--- a/arch/sh/drivers/pci/ops-sh7786.c
+++ b/arch/sh/drivers/pci/ops-sh7786.c
@@ -1,7 +1,7 @@
 /*
  * Generic SH7786 PCI-Express operations.
  *
- *  Copyright (C) 2009  Paul Mundt
+ *  Copyright (C) 2009 - 2010  Paul Mundt
  *
  * This file is subject to the terms and conditions of the GNU General Public
  * License v2. See the file "COPYING" in the main directory of this archive
@@ -25,32 +25,39 @@ static int sh7786_pcie_config_access(unsigned char access_type,
 		struct pci_bus *bus, unsigned int devfn, int where, u32 *data)
 {
 	struct pci_channel *chan = bus->sysdata;
-	int dev, func;
+	int dev, func, type;
 
 	dev = PCI_SLOT(devfn);
 	func = PCI_FUNC(devfn);
+	type = !!bus->parent;
 
 	if (bus->number > 255 || dev > 31 || func > 7)
 		return PCIBIOS_FUNC_NOT_SUPPORTED;
-	if (devfn)
+	if (bus->parent == NULL && dev)
 		return PCIBIOS_DEVICE_NOT_FOUND;
 
+	/* Clear errors */
+	pci_write_reg(chan, pci_read_reg(chan, SH4A_PCIEERRFR), SH4A_PCIEERRFR);
+
 	/* Set the PIO address */
 	pci_write_reg(chan, (bus->number << 24) | (dev << 19) |
 				(func << 16) | (where & ~3), SH4A_PCIEPAR);
 
 	/* Enable the configuration access */
-	pci_write_reg(chan, (1 << 31), SH4A_PCIEPCTLR);
+	pci_write_reg(chan, (1 << 31) | (type << 8), SH4A_PCIEPCTLR);
+
+	/* Check for errors */
+	if (pci_read_reg(chan, SH4A_PCIEERRFR) & 0x10)
+		return PCIBIOS_DEVICE_NOT_FOUND;
+	/* Check for master and target aborts */
+	if (pci_read_reg(chan, SH4A_PCIEPCICONF1) & ((1 << 29) | (1 << 28)))
+		return PCIBIOS_DEVICE_NOT_FOUND;
 
 	if (access_type == PCI_ACCESS_READ)
 		*data = pci_read_reg(chan, SH4A_PCIEPDR);
 	else
 		pci_write_reg(chan, *data, SH4A_PCIEPDR);
 
-	/* Check for master and target aborts */
-	if (pci_read_reg(chan, SH4A_PCIEPCICONF1) & ((1 << 29) | (1 << 28)))
-		return PCIBIOS_DEVICE_NOT_FOUND;
-
 	return PCIBIOS_SUCCESSFUL;
 }
 
@@ -69,8 +76,10 @@ static int sh7786_pcie_read(struct pci_bus *bus, unsigned int devfn,
 	spin_lock_irqsave(&sh7786_pcie_lock, flags);
 	ret = sh7786_pcie_config_access(PCI_ACCESS_READ, bus,
 					devfn, where, &data);
-	if (ret != PCIBIOS_SUCCESSFUL)
+	if (ret != PCIBIOS_SUCCESSFUL) {
+		*val = 0xffffffff;
 		goto out;
+	}
 
 	if (size == 1)
 		*val = (data >> ((where & 3) << 3)) & 0xff;
diff --git a/arch/sh/drivers/pci/pcie-sh7786.c b/arch/sh/drivers/pci/pcie-sh7786.c
index 78f378731858..d053ffca8196 100644
--- a/arch/sh/drivers/pci/pcie-sh7786.c
+++ b/arch/sh/drivers/pci/pcie-sh7786.c
@@ -148,16 +148,11 @@ static int pci_wait_for_irq(struct pci_channel *chan, unsigned int mask)
 static void phy_write_reg(struct pci_channel *chan, unsigned int addr,
 			  unsigned int lane, unsigned int data)
 {
-	unsigned long phyaddr, ctrl;
+	unsigned long phyaddr;
 
 	phyaddr = (1 << BITS_CMD) + ((lane & 0xf) << BITS_LANE) +
 			((addr & 0xff) << BITS_ADR);
 
-	/* Enable clock */
-	ctrl = pci_read_reg(chan, SH4A_PCIEPHYCTLR);
-	ctrl |= (1 << BITS_CKE);
-	pci_write_reg(chan, ctrl, SH4A_PCIEPHYCTLR);
-
 	/* Set write data */
 	pci_write_reg(chan, data, SH4A_PCIEPHYDOUTR);
 	pci_write_reg(chan, phyaddr, SH4A_PCIEPHYADRR);
@@ -165,20 +160,22 @@ static void phy_write_reg(struct pci_channel *chan, unsigned int addr,
 	phy_wait_for_ack(chan);
 
 	/* Clear command */
+	pci_write_reg(chan, 0, SH4A_PCIEPHYDOUTR);
 	pci_write_reg(chan, 0, SH4A_PCIEPHYADRR);
 
 	phy_wait_for_ack(chan);
-
-	/* Disable clock */
-	ctrl = pci_read_reg(chan, SH4A_PCIEPHYCTLR);
-	ctrl &= ~(1 << BITS_CKE);
-	pci_write_reg(chan, ctrl, SH4A_PCIEPHYCTLR);
 }
 
 static int phy_init(struct pci_channel *chan)
 {
+	unsigned long ctrl;
 	unsigned int timeout = 100;
 
+	/* Enable clock */
+	ctrl = pci_read_reg(chan, SH4A_PCIEPHYCTLR);
+	ctrl |= (1 << BITS_CKE);
+	pci_write_reg(chan, ctrl, SH4A_PCIEPHYCTLR);
+
 	/* Initialize the phy */
 	phy_write_reg(chan, 0x60, 0xf, 0x004b008b);
 	phy_write_reg(chan, 0x61, 0xf, 0x00007b41);
@@ -187,9 +184,15 @@ static int phy_init(struct pci_channel *chan)
 	phy_write_reg(chan, 0x66, 0xf, 0x00000010);
 	phy_write_reg(chan, 0x74, 0xf, 0x0007001c);
 	phy_write_reg(chan, 0x79, 0xf, 0x01fc000d);
+	phy_write_reg(chan, 0xb0, 0xf, 0x00000610);
 
 	/* Deassert Standby */
-	phy_write_reg(chan, 0x67, 0xf, 0x00000400);
+	phy_write_reg(chan, 0x67, 0x1, 0x00000400);
+
+	/* Disable clock */
+	ctrl = pci_read_reg(chan, SH4A_PCIEPHYCTLR);
+	ctrl &= ~(1 << BITS_CKE);
+	pci_write_reg(chan, ctrl, SH4A_PCIEPHYCTLR);
 
 	while (timeout--) {
 		if (pci_read_reg(chan, SH4A_PCIEPHYSR))
@@ -287,6 +290,9 @@ static int pcie_init(struct sh7786_pcie_port *port)
 	__raw_writel(memphys, chan->reg_base + SH4A_PCIELAR0);
 	__raw_writel((memsize - SZ_256) | 1, chan->reg_base + SH4A_PCIELAMR0);
 
+	__raw_writel(memphys, chan->reg_base + SH4A_PCIEPCICONF4);
+	__raw_writel(0, chan->reg_base + SH4A_PCIEPCICONF5);
+
 	/* Finish initialization */
 	data = pci_read_reg(chan, SH4A_PCIETCTLR);
 	data |= 0x1;