I've used the full D1 KDVD template (NTSC) for a few weeks now with no problems. Adverage encode time for a DivX is about 7 hours. However the last few days the encoding time is taking 15 hours. I checked TMPGenc settings with the template to see if I had "accidentaly" made any chages. I see motion search precision is set to highest quality (very slow) where as on the PaL template it is set to high quality (slow). Should the NTSC template setting be high quality too? Is this the problem?

Thanks in advance.

Use high quality. Highest quality is known to produce more artfacts, take more time and produce bigger filesize for the same CQ.