What is the question?
SPAN'd ports will show as up/down(monitoring) because they aren't passing traffic, they simply receive. They behave differently because of the SPAN.
As far as the not able to connect bit, is it sporadic or predictable? Are you seeing CPU hits on the switch or server? What is the utilization like on the switchport?
Typically you should have a separate management port for the server than the same port that processes the traffic dump.
CPU hits on the switch or server was minor at that that when i face this problem only one user active on this swiched connected network
in same time i face same issue, and this will resolve temoprarly bu using no monitor session 1..... and again put full command, shut interface and again
no shut interface