Sorry for the trouble this is causing! I seem to remember there being a performance issue in previous versions when the inbox contained a large number of items, but I believe that's been fixed.
There is an open item on quick entry performance when there are a large number (more than a thousand, for example) projects in the database.
The best thing to do here is likely to email the
support ninjas; we can run a 'sample' report on your machine that will give us information on exactly what code is being executed...