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After running an application two or three times, communication stops
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It is always recommended that you close a file handle obtained by FT_Open/FT_OpenEx before exiting an application. Side effects of not closing the handle with the multithreaded setting (as illustrated above) can be future communication with the device fails (always test this prior to enabling this setting). The Sample applications demonstrate a method of trapping an abnormal exit (control C operation) and closing each handle in turn.

If you cannot find a work around then try setting the
USB Reset After Open
bit in the ftd2xx.cfg file but only as a last resort.