Some motherboards had a hard time "waking up" as you describe. My older Core2Duo system had that exact problem as you describe. Ended up leaving on all of the time unit I was able to replace it. My other systems never seemed to have that problem.
Ross
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In SI, a little termination and attention to layout goes a long way. In EMC, without SI, you'll spend 80% of the effort on the last 3dB.
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