Check if you have enabled CONFIG_PCI_AARDVARK (=y or =m) and in case it is =m then check if you have loaded pci-aardvark.ko module. This is driver for PCIe controller.
Basically for Marvell Armada 3720 boards you need these options:
CONFIG_AHCI_MVEBU
CONFIG_ARCH_MVEBU
CONFIG_ARMADA_37XX_CLK
CONFIG_ARMADA_37XX_RWTM_MBOX
CONFIG_ARMADA_37XX_WATCHDOG
CONFIG_ARM_ARMADA_37XX_CPUFREQ
CONFIG_CRYPTO_DEV_SAFEXCEL
CONFIG_GPIO_MOXTET
CONFIG_I2C_PXA
CONFIG_MARVELL_PHY
CONFIG_MMC_SDHCI_XENON
CONFIG_MOXTET
CONFIG_MVMDIO
CONFIG_MVNETA
CONFIG_NET_DSA_MV88E6XXX
CONFIG_PCI_AARDVARK
CONFIG_PHY_MVEBU_A3700_COMPHY
CONFIG_PHY_MVEBU_A3700_UTMI
CONFIG_PINCTRL_ARMADA_37XX
CONFIG_SERIAL_MVEBU_CONSOLE
CONFIG_SERIAL_MVEBU_UART
CONFIG_SPI_ARMADA_3700
CONFIG_TURRIS_MOX_RWTM
CONFIG_USB_EHCI_HCD_ORION
CONFIG_USB_XHCI_MVEBU
So check that you have all of them enabled.
