This only seems to be affecting one user. He has a NIS account and has tried 2 NIS accounts to make sure. He's running a Mac with the latest X2Go (2.7.11) connecting to a Fedora 25 server with NIS, choosing the MATE desktop and audio disabled. We made sure to check the security settings as per this older post screenshot and confirmed the .Xauthority permissions problem does not exist. Here are some debug-enabled logs.

Feb 16 21:11:57 ourserver /usr/bin/x2gostartagent: x2gostartagent called with options: 800x600 adsl 16m-jpeg-9 unix-kde-depth_32 us query 0 D MATE both

Feb 16 21:11:57 ourserver /usr/bin/x2gosessionlimit[25474]: x2gosessionlimit has been called

Feb 16 21:11:57 ourserver /usr/bin/x2golistsessions[25477]: x2golistsessions has been called with options: --all-servers

Feb 16 21:11:59 ourserver /usr/sbin/x2gocleansessions[26305]: NISuser-64-1487297518_stDMATE_dp32: state file for this session does not exist: /tmp/.x2go-NISuser/C-NISuser-64-1487297518_stDMATE_dp32/state (this can be ignored during session startups)

Feb 16 21:12:00 ourserver /usr/bin/x2gofeature: x2gofeature called with options: X2GO_RUN_EXTENSIONS

Feb 16 21:12:00 ourserver /usr/share/x2go/x2gofeature.d/x2goserver-extensions.features: x2goserver-extensions.features called with options: X2GO_RUN_EXTENSIONS

Feb 16 21:12:00 ourserver /usr/bin/x2goserver-run-extensions: x2goserver-run-extensions called with options: NISuser-64-1487297518_stDMATE_dp32 pre-start

Feb 16 21:12:00 ourserver /usr/bin/x2gostartagent: successfully started X2Go agent session with ID NISuser-64-1487297518_stDMATE_dp32

Feb 16 21:12:00 ourserver /usr/bin/x2gofeature: x2gofeature called with options: X2GO_RUN_EXTENSIONS

Feb 16 21:12:00 ourserver /usr/share/x2go/x2gofeature.d/x2goserver-extensions.features: x2goserver-extensions.features called with options: X2GO_RUN_EXTENSIONS

Feb 16 21:12:00 ourserver /usr/bin/x2goserver-run-extensions: x2goserver-run-extensions called with options: NISuser-64-1487297518_stDMATE_dp32 post-start

Feb 16 21:12:01 ourserver /usr/bin/x2gostartagent: blocking creation of agent's keyboard file /tmp/.x2go-NISuser/C-NISuser-64-1487297518_stDMATE_dp32/keyboard as requested by session startup command

Feb 16 21:12:05 ourserver audit: CRYPTO_KEY_USER pid=25308 uid=0 auid=xxxx ses=916 msg='op=destroy kind=server fp=SHA256:ed:ac:95:b9:6d:a7:65:a8:79:a8:79:4e:41:3c:6b:58:c8:5b:37:10:c1:6a:bc:8f:2f:1c:f1:00:98:4f:2a:78 direction=? spid=25774 suid=xxxx exe="/usr/sbin/sshd" hostname=? addr=? terminal=? res=success'

Feb 16 21:12:05 ourserver /usr/bin/x2gocmdexitmessage: x2gocmdexitmessage called with options: NISuser-64-1487297518_stDMATE_dp32

Feb 16 21:12:05 ourserver audit: USER_END pid=25308 uid=0 auid=xxxx ses=916 msg='op=PAM:session_close grantors=pam_selinux,pam_loginuid,pam_selinux,pam_namespace,pam_keyinit,pam_keyinit,pam_limits,pam_systemd,pam_unix acct="NISuser" exe="/usr/sbin/sshd" hostname=ipaddress addr=ipaddress terminal=ssh res=success'

Feb 16 21:12:05 ourserver audit: CRED_DISP pid=25308 uid=0 auid=xxxx ses=916 msg='op=PAM:setcred grantors=pam_unix acct="NISuser" exe="/usr/sbin/sshd" hostname=ipaddress addr=ipaddress terminal=ssh res=success'

Feb 16 21:12:05 ourserver audit: USER_END pid=25308 uid=0 auid=xxxx ses=916 msg='op=login id=xxxx exe="/usr/sbin/sshd" hostname=ipaddress addr=ipaddress terminal=ssh res=success'

Feb 16 21:12:05 ourserver audit: USER_LOGOUT pid=25308 uid=0 auid=xxxx ses=916 msg='op=login id=xxxx exe="/usr/sbin/sshd" hostname=ipaddress addr=ipaddress terminal=ssh res=success'