I have several other Routers, same setup in general, the difference is ROS versions.
Examples of my x86 machine versions:
4.11 - Has the same number of Vlans as the v5.1 in question, no problems.
4.30 - Not as many Vlans but using hotpots.
4.60 - Not as many Vlans but more traffic and pps.
I have been considering actually going backwards in versions and going back down to like v4.11 or something.
Also the hardware this is on is an i2600, 8GB Ram. Others have reported some issues with v5 of ROS, one of which I actually replied to and one of which I started and thought I had fixed.
http://forum.mikrotik.com/t/x86-ros-5-14-randomly-crash-on-vmware/58822/1
http://forum.mikrotik.com/t/tx-drops-on-vlan-interfaces/58818/1 (I made this post awhile ago, no responses)