The button element has User Agent Styles for text and background color. If you set these to something else, but also have a transition on those properties, you will see a transition on page load. This transition will change from the user agent style, to the style you set. This ONLY applies if you are using a linked style sheet. Which, you are, because you don't want to have to update styles on multiple pages. I assume this is not restricted to the button element, that's just my example.
My biggest problem was that this caused my buttons to change size because I had the transition set to 'all'. I changed it to only affect the required properties, and the brief color change is much less noticeable.
Maybe someone will bump into this and save themselves a headache.