not entirely understanding the description but in general unless you explicitly enforce the join between two 'tables' in crystal it only becomes enforced if you use a field (in any capacity) from both tables (or ends of daisy-chained tables). So if you drag and drop a field onto the canvas you can see your data set wildly change it is because the join is being enforced. If there is no join it will act like a cartesian join/product which can make your data set huge and also make the report run really slow. Also sub-reports and page numbering can also greatly impact performance.

Thanks guys - the queries work fine independently its the fact that Im querying 2 separate databases but are joined by an inner join and this is causing some slowness effectively joining using the crystal report rather than SQL to create the report.

Unless I am mistaken I cant run the query within SQL Management studio given that only links\queries a single databases\table unless I create a join.