Sorry, I'm doing this from memory as I currently have no switch-based VLANs running on my routers and have no spare hardware I can test with, so bear with me here.
I went through exports of my old configuration where I did use switch based VLAN and found I had explicitly set the vlan-header attribute (RB1100AHx2, different chip but it should work on yours as well).
I used 'vlan-header=always-strip' on access ports. On the the trunk port I used 'vlan-header=add-if-missing' but I believe you should be tagging it as a hybrid by using by using 'vlan-header=leave-as-is'.
So try
/interface ethernet
set ether3 master-port=ether2
set ether4 master-port=ether2
/interface ethernet switch vlan
add vlan-id=1 switch=switch1 ports=ether2,ether3
add vlan-id=200 switch=switch1 ports=ether2,ether4
/interface ethernet switch port
set ether2 vlan-mode=secure default-vlan-id=1 vlan-header=leave-as-is
set ether3 vlan-mode=secure default-vlan-id=1 vlan-header=always-strip
set ether4 vlan-mode=secure default-vlan-id=200 vlan-header=always-strip
EDIT:
Reading the Wiki more closely,
http://wiki.mikrotik.com/wiki/Manual:Sw ... d_Ports.29 states:
VLAN Hybrid ports which can forward both tagged and untagged traffic are supported only by some Gigabit switch chips (QCA8337, AR8327)
Your RB941-2nD uses the AR8227, so according to this information, it can't do hybrid ports.