OK so we've done quite a bit more digging on this issue and it seems to be the installer runs ok but using the configuration does not populate the registry properly.
After a fresh install the registry only has a few keys for windows integration, then once the configuration is run (In Word etc) the details of the server etc are then set in the registry, this is where we seem to run into the issue. We run Kaspersky disk encryption and AV on laptops so I think it is to do with this as on other dekstops still with the AV but no disk encryption we do not get the issue,
Can someone explain the process of what touches what during the configuration,
1, User adds the necessary url and alias into the DTI Configuration Dialogue
2, DTI Checks the connection
3, Windchill prompts for Username and Password
4, DTI writes the details to the registry
5, User can then select the active server
Is there something happening between 2 and 4 that could be affected by AV or a permission or similar?
Heres a curve ball, we put Fiddler onto the laptop that was having the issue, rerun the configuration, then entered the username and pw and we could then select the active server and it worked ?????????? apparently when running fiddler it interfaces between ie and the network.
Curious, so will post an answer as soon as we get one
Oh and one more thing, the uninstaller didn't seem to remove all the registry keys from the laptop, we restored the laptop to an earlier date and compared the two registries.