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A few questions...
You said this was a new application, does the old application get completely calculated or is intelligent calc (blocks already calculated are not recalculated) on?
The second, new application, may have to be calculated in full and then the next calculation will see the calculated blocks and ignore. can you post the entire calculation script or is this business rules/calc manager calcualtions?
did you compare the data and index cache settings on the new appliction with the old application?
Is there enough memory for both to be loaded on the server?
How big are the blocks in both applications ?
It's possible that those 15 extra accounts made the block size in the new application exceed a certain threshold that makes calculation take much longer.
That's the only difference I can think of if you have already made sure that everything else was the same in both applications.