Not sure if this is related but "pacman -Syu" on my GoFlex Home also errors with the following:
$this->bbcode_second_pass_code('', '
Targets (14): filesystem-2012.6-2 git-1.7.10.4-1 gnutls-3.0.20-1
initscripts-2012.06.1-1 krb5-1.10.2-1 libcups-1.5.3-4
libwbclient-3.6.5-3 linux-api-headers-3.3.8-1 openntpd-3.9p1-15
pacman-mirrorlist-20120608-1 psmisc-22.17-1 samba-3.6.5-3
smbclient-3.6.5-3 systemd-tools-185-1
Total Installed Size: 141.92 MiB
Net Upgrade Size: 0.12 MiB
Proceed with installation? [Y/n]
(14/14) checking package integrity [######################] 100%
(14/14) loading package files [######################] 100%
(14/14) checking for file conflicts [######################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /var/lock exists in filesystem
filesystem: /var/run exists in filesystem
Errors occurred, no packages were upgraded.
')
EDIT: It seems this is an issue across the archlinux platform with a solution posted
here.