I am getting the exact same issue, however running it as root works (except it's obviously not what I want, because I'd lose all my config from $HOME on every app I'd launch with synapse):

[138] ~/Tools/synapse-0.2.10 [master] $ synapse
[INFO 00:09:54.142944] [synapse-main:268] Starting up...
[INFO 00:09:54.233155] [synapse-main:211] Binding activation to <Control><Super>s
[INFO 00:09:54.254721] [view-base:251] Screen is composited.
[INFO 00:09:54.255503] [controller:59] Using xim input method.
[WARN 00:09:54.328466] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/kde4/knetattach.desktop
[WARN 00:09:54.329435] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/kde4/calligra.desktop
[WARN 00:09:54.338936] [desktop-file-service:193] Unable to get exec for Photos lens for Unity
[WARN 00:09:54.349859] [desktop-file-service:193] Key file contains key 'Terminal' which has a value that cannot be interpreted.
[WARN 00:09:54.354821] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/gnome-deja-dup-panel.desktop
[WARN 00:09:54.356838] [desktop-file-service:193] Unable to get exec for Evolution Data Server
[WARN 00:09:54.364194] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/vim.desktop
[INFO 00:09:54.377968] [gnome-session-plugin:158] org.gnome.SessionManager is available
[WARN 00:09:54.408473] [ssh-plugin:116] /home/baboon/.ssh/config: Error opening file: No such file or directory
[INFO 00:09:54.429216] [hybrid-search-plugin:179] keeps in cache now 95 file names
Segmentation fault (core dumped)
[139] ~/Tools/synapse-0.2.10 [master] $ sudo synapse
[INFO 00:09:58.607797] [synapse-main:268] Starting up...
[INFO 00:09:58.707206] [synapse-main:211] Binding activation to <Control><Super>s
[INFO 00:09:58.725724] [view-base:251] Screen is composited.
[INFO 00:09:58.726637] [controller:59] Using gtk-im-context-simple input method.
[WARN 00:09:58.842825] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/kde4/knetattach.desktop
[WARN 00:09:58.843612] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/kde4/calligra.desktop
[WARN 00:09:58.853358] [desktop-file-service:193] Unable to get exec for Photos lens for Unity
[WARN 00:09:58.864708] [desktop-file-service:193] Key file contains key 'Terminal' which has a value that cannot be interpreted.
[WARN 00:09:58.867541] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/gnome-sudoku.desktop
[WARN 00:09:58.868217] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/gnome-mines.desktop
[WARN 00:09:58.868439] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/gnome-mahjongg.desktop
[WARN 00:09:58.869529] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/gnome-deja-dup-panel.desktop
[WARN 00:09:58.872103] [desktop-file-service:193] Unable to get exec for Evolution Data Server
[WARN 00:09:58.879802] [desktop-file-service:193] Unable to create AppInfo for /usr/share/applications/vim.desktop
[WARN 00:09:58.906963] [ssh-plugin:116] /home/baboon/.ssh/config: Error opening file: No such file or directory
[INFO 00:09:58.936685] [hybrid-search-plugin:179] keeps in cache now 95 file names
[WARN 00:10:00.328553] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity
[WARN 00:10:00.448186] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity
[WARN 00:10:00.536328] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity
[WARN 00:10:00.568257] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity
[WARN 00:10:00.712528] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity
[WARN 00:10:00.777017] [zeitgeist-plugin:740] Zeitgeist search failed: GDBus.Error:org.freedesktop.DBus.Error.UnknownMethod: No such interface 'org.gnome.zeitgeist.Index' on object at path /org/gnome/zeitgeist/index/activity