Hello
This often happens depending on the user connection and/or user-to-server rapidity.
The "custom color" code is stocked in "skin.css.php" which is downloaded by the page once it's fully loaded, this explains the latency.
Some websites that has cache CDN do not have this issue since the page is already loaded without redownloading that skin file, but others do not.
This is a point which needs improvement in the next updates in order to cancel/reduce the latency.
