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The problem with the Starter edition is not the simulation speed (close to 40% of PE/DE) but the instance limit, if you hit this limit (which I suspect you do with a PCIe core) your simulation speed will effectively grind to a halt (1% of PE/DE speed). You should get a warning that you have hit this limit, if not check your simulation speed (using the simstats command) and the beginning and end of your simulation, you should see quite a difference.
As KTan9 mentioned you need to purchase either the Intel-Modelsim version or the full PE/DE version from Mentor which is not cheap but does not have any speed restrictions and comes with a lot of other goodies such as code coverage. Modelsim DE has (amongst others) full assertion support which can be used for functional verification.
Good luck,
Hans.
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