I found a problem with the way the license files are generated by VMware and read by the license server.
I was checking the current licensing numbers via VirtualCenter and the FlexLM license server. It was showing there were 8 x 1/cpu for each product (ESX, HA, DRS etc). This is double what it actually shows in the license portal.
I double checked what I was supposed to have and it is indeed 4 x 1/cpu licenses. I have found that each time a license file is generated via the vmware portal, if the license file is added with the old one and reloaded, it adds the licenses together, hence 8.
Now I know the cause, I have removed all the files and just have the one generated license file now which is correct (4 x 1/cpu).
I made VMware support aware, as anyone out there who is not so honest may be able to take advantge of this licensing flaw. but it took some explaining to two different people. One first said that it is supposed to show as double in VirtualCenter! Anyway if you inherit a VI from anyone and see more licenses than you thought you had, its probably not right, check it.