MDS switch offers 8000 zones per switch with 16,000 zone members per physical fabric (includes all VSANs)

Please refer to configuration limit guide.

http://www.cisco.com/en/US/docs/switches/datacenter/mds9000/sw/nx-os/configuration/guides/limits/limits_42x.html

Zone Member Configuration Guidelines are even more important to optimize the resource usage on the switch.

Zone config best practice clearly indicates:

"The best practice is to avoid configuring large number of targets and or or large numbers of initiators in a single zone. Such configuration wastes switch resources by provisioning and managing many communicating pairs (initiator-to-initiator or target-to-target) which will never actually communicate with each other. For this reason, single initiator with a single target is the most efficient approach to zoning."

The following guidelines must be considered when creating zone members:

•Configuring only one initiator and one target for a zone provides most efficient use of the switch resources.

•Configuring the same initiator to multiple targets is accepted.

•Configuring multiple initiators to multiple targets is not recommended.

http://www.cisco.com/en/US/docs/switches/datacenter/mds9000/sw/4_1/configuration/guides/cli_4_1/zone.html#wp1967293

If the zone activation or changes run into issues off and on..quite possibly the zoning configuration best practices could be lacking.