I`ve set up a Netconsole to compare bootup process between the two cases but the output looks identical and bootable USB is correctly detected in both cases.

Is it the famous issue of not booting from the correct USB I`m facing?
$this->bbcode_second_pass_code('', 'USB EHCI 1.00
scanning bus for devices... 3 USB Device(s) found
scanning bus for storage devices... 1 Storage Device(s) found
Loading file "/rescueme" from usb device 0:1 (usbda1)
** File not found /rescueme
reading /rescueme.txt
** Unable to read "/rescueme.txt" from usb 0:1 **
Creating 1 MTD partitions on "nand0":
0x000002500000-0x000008000000 : "mtd=3"
UBI: attaching mtd1 to ubi0
UBI: physical eraseblock size: 131072 bytes (128 KiB)
UBI: logical eraseblock size: 129024 bytes
UBI: smallest flash I/O unit: 2048
UBI: sub-page size: 512
UBI: VID header offset: 512 (aligned 512)
UBI: data offset: 2048
UBI: attached mtd1 to ubi0
UBI: MTD device name: "mtd=3"
UBI: MTD device size: 91 MiB
UBI: number of good PEBs: 728
UBI: number of bad PEBs: 0
UBI: max. allowed volumes: 128
UBI: wear-leveling threshold: 4096
UBI: number of internal volumes: 1
UBI: number of user volumes: 0
UBI: available PEBs: 717
UBI: total number of reserved PEBs: 11
UBI: number of PEBs reserved for bad PEB handling: 7
UBI: max/mean erase counter: 1/1
UBIFS error (pid 0): ubifs_get_sb: cannot open "ubi:rootfs", error -19
Error reading superblock on volume 'ubi:rootfs'!
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
1 bytes read
Found bootable drive on usb 0:1
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
4549504 bytes read
Loading file "/boot/uInitrd" from usb device 0:1 (usbda1)
** File not found /boot/uInitrd
## Booting kernel from Legacy Image at 00800000 ...
Image Name: Linux-4.4.1-1-ARCH
Image Type: ARM Linux Kernel Image (uncompressed)
Data Size: 4549440 Bytes = 4.3 MiB
Load Address: 00008000
Entry Point: 00008000
Verifying Checksum ... OK
Loading Kernel Image ... OK
OK
Using machid 0xdd6 from environment
Starting kernel ...')
$this->bbcode_second_pass_code('', '[admin@WL-Asus root]$ nc -u -l -p 6666
U-Boot 2011.12 (Feb 20 2012 - 21:21:59)
Pogoplug E02
arm-none-linux-gnueabi-gcc (Sourcery G++ Lite 2009q3-67) 4.4.1
GNU ld (Sourcery G++ Lite 2009q3-67) 2.19.51.20090709
Hit any key to stop autoboot: 0
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 4 USB Device(s) found
scanning bus for storage devices... 2 Storage Device(s) found
stopping USB..
(Re)start USB...
USB: Register 10011 NbrPorts 1
USB EHCI 1.00
scanning bus for devices... 4 USB Device(s) found
scanning bus for storage devices... 2 Storage Device(s) found
Loading file "/rescueme" from usb device 0:1 (usbda1)
** File not found /rescueme
reading /rescueme.txt
** Unable to read "/rescueme.txt" from usb 0:1 **
Creating 1 MTD partitions on "nand0":
0x000002500000-0x000008000000 : "mtd=3"
UBI: attaching mtd1 to ubi0
UBI: physical eraseblock size: 131072 bytes (128 KiB)
UBI: logical eraseblock size: 129024 bytes
UBI: smallest flash I/O unit: 2048
UBI: sub-page size: 512
UBI: VID header offset: 512 (aligned 512)
UBI: data offset: 2048
UBI: attached mtd1 to ubi0
UBI: MTD device name: "mtd=3"
UBI: MTD device size: 91 MiB
UBI: number of good PEBs: 728
UBI: number of bad PEBs: 0
UBI: max. allowed volumes: 128
UBI: wear-leveling threshold: 4096
UBI: number of internal volumes: 1
UBI: number of user volumes: 0
UBI: available PEBs: 717
UBI: total number of reserved PEBs: 11
UBI: number of PEBs reserved for bad PEB handling: 7
UBI: max/mean erase counter: 1/1
UBIFS error (pid 0): ubifs_get_sb: cannot open "ubi:rootfs", error -19
Error reading superblock on volume 'ubi:rootfs'!
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
1 bytes read
Found bootable drive on usb 0:1
Loading file "/boot/uImage" from usb device 0:1 (usbda1)
4549504 bytes read
Loading file "/boot/uInitrd" from usb device 0:1 (usbda1)
** File not found /boot/uInitrd
## Booting kernel from Legacy Image at 00800000 ...
Image Name: Linux-4.4.1-1-ARCH
Image Type: ARM Linux Kernel Image (uncompressed)
Data Size: 4549440 Bytes = 4.3 MiB
Load Address: 00008000
Entry Point: 00008000
Verifying Checksum ... OK
Loading Kernel Image ... OK
OK
Using machid 0xdd6 from environment
Starting kernel ...')