Hi shodruk,
please find below the output of the 2 commands. Today I observed a similar initial string of 9-10 reboots with USB not working, followed by 7-8 reboots with a working USB. Again, USB does not work if and only if dmesg displays
xusbps-dr e0002000.usb: Unable to init USB phy, missing?
and lsusb gives error -99, whereas USB does work if and only if dmesg gives
xusbps-ehci xusbps-ehci.0: Xilinx PS USB EHCI Host Controller
xusbps-ehci xusbps-ehci.0: new USB bus registered, assigned bus number 1
...
In the latter case, lsusb gives
Bus 001 Device 002: ID 046d:c52b Logitech, Inc. Unifying Receiver
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
and both keyboard and mouse of my Logitech mk520 wireless combo work flawlessly with the board. Actually, whenever the USB was working, I was able to connect and use two other (wired, USB) keyboards and two other (wired, USB) mice. For instance, I have just unplugged the combo and plugged an old mouse and lsusb gives
Bus 001 Device 003: ID 0461:4d03 Primax Electronics, Ltd Kensington Mouse-in-a-box
Plugging a USB keyboard gives then
Bus 001 Device 004: ID 045e:00dd Microsoft Corp. Comfort Curve Keyboard 2000 V1.0
So in my case it really looks like a boot-time problem. The only pattern which I have observed is that USB somehow decides to keep functioning for all reboots after a few initial consecutive reboots where it does not, so when the board is "warmed up". Might this be simply a matter of temperature of the board? Having devices plugged or not at boot time does not seem to influence the course of events. I'll keep experimenting....
linaro-nano:~> cat /proc/cmdline
root=/dev/mmcblk0p2 rw rootfstype=ext4 rootwait devtmpfs.mount=1 video=HDMI-A-1:1280x720@60
linaro-nano:~> cat /etc/X11/xorg.conf
Section "Device"
Identifier "Card0"
Driver "modesetting"
Option "ShadowFB" "True"
Option "SWCursor" "True"
Option "HWCursor" "False"
EndSection
Section "Screen"
Identifier "Screen0"
Device "Card0"
SubSection "Display"
#---- Uncomment your preferred mode ----
#Modes "1920x1200"
#Modes "1920x1080"
Modes "1280x720"
#Modes "640x480"
EndSubSection
EndSection