Hi Martin,
Gradebook is computationally intensive and checks all students and every assessment point at the same time. It sounds like you are exceeding the permitted time for a php script to run and this is why you see different things for different students. Removing students and reducing assement items in a course will fix this but is not always practical - sometime splitting the course to term1 term2 might be easier. Increasing the php execution time in php.ini will allow the script to run but obviously increases server load and decreases performance elsewhere.
Gradebook
A long wait for grades to come up
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