For information I think we have figured this out. We believe that SCOM is reading the volume latency in Microseconds rather than Milliseconds. We have been looking in NetApp Management Console System Performance Monitoring and noticed that it is displaying volume latency in Microseconds. There are 1000 Microseconds to 1 millisecond and when we compare Management Console to SCOM the figures being reported are more aligned to the Microseconds readings rather than milliseconds.
I've created overrides for 10000 for critical instead of 10 and 5000 for warning instead of 5.
To confuse matters more the LUN latency in mangaement consoles are monitored in Milliseconds!!
I don't know if i've read the MP documentation wrong but hopefully this may help some people in the future.