If you are describing a network outage due to traffic storm then it's possible that the channel was misconfigured and caused a spanning tree loop. Are you doing channel and trunking? Or are these links for a single vlan? Was removing the fiber links and reconnecting them the only actions taken to resolve? That is, you removed only this new channel's fiber links (breaking a possible loop) and placed them in new access ports and all was well? If so, check your configs and spanning tree topology for any issues.
Remember for port channeling partner links on the same chassis and peer must match physical characteristics and software configuration. That is, if you have an interface hard coded for 100/Full then it's parter on the same chassis must have same settings and capability. The other device you are channeling to must also have same configuration. If one port is configured for trunking in the channel then all ports of the channel must be configured for trunking.
http://www.cisco.com/univercd/cc/td/doc/product/lan/c2900xl/29_35wc6/scg/swports.htm