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Find usages not working reliably.

There seems to be an issue with find usages not reliably finding all usages.
I am using the latest EAP for phpstorm 6.

I right click on the function (the scope is set to project) and it says there are no usages.  Later on I am working on something else and find usages of the function that phpstorm said werent there.
After further tinkering it seems as if (even though I have the scope set to project) it is only searching files that are open in a tab.

If I open the tab, it finds the usages.
If I close that tab, it can no longer find the usages.

I have the scope set to search the whole project (find usages settings) but that doesnt appear to be what is actually happening.

Has anyone else experienced this?  Is there a work around?

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