Might Mavericks interfere with long computations?
According to the Apple Developer documentation (and Core Technologies Overview for Mavericks), App Nap can be opted out by either an Application developer or a user, but by default are active. 

For a GUI application, the user can opt an application out of App Nap manually with a checkbox in the Finder “Get Info...” pane.

Timer Coalescing only becomes active when on battery power, so it should not affect your long running background processes.

Finally, you can check on the status of App Nap in the Activity Monitor. On the Energy Tab, there is a column describing App Nap status for each application, so if policies change, you can check actual status here.