The most likely reason a nocking point is altered when brace height is changed is because the string wasn't made properly. When the body of a string doesn't have any twists in it, the strands that make up each bundle should not be wrapped around each other. This helps the string lay "round" once the body is twisted. If the bundles are already wrapped/twisted themselves prior to adding twists to the body, then when you twist the body it is unlikely those twists would be evenly distributed as they are going to be distributed in a manner that works in a manner that offers the least amount of resistence against the "pre-wrapped" up bundles.
The way one can confirm this is by removing all the twists from the string and holding it straight. When this is done, not only should the bundles be easily seperated, but the strands within the bundles should also be easily seperated. If the bundles are wrapped, the string was made wrong and it is possible that these bundles have more twists on one side of the string's serving than on the other side as it is unlikely those twists were evenly distributed prior to serving the string (since it was made by someone that doesn't know how to properly make a flemish string).