EPMA application app compare reporting incorrectly

Hi,
we've just started using 11.1.2.3 for Planning Apps and ASO cubes. One thing that has changed is the ability to refresh security from within the planning application. So we now do the same refresh from within the application library just asking to create filters. However when we do this  the subsequent application compares show the apps as having no metadata differences and the library says that they are in sync - which they are but the changes that we didn't ask to be deployed are in the planning app but not the Essbase app - any ideas why might occur? Or are there alternatives for this sort of security refresh.?
Thanks,
Jeremy.

To clarify the original post - the way to avoid this the is to use the Manage->Database option from within planning that option has not gone (but still doesn't explain the behaviour of the deploy)

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