Hi Dan,
Yes there was a change to the Custom Totara theme (T-11802 Fixed Customtotara Theme issue where certain background colours could make headings hard to read) that would have overwritten your CSS. This patch was added as it was possible to make the background color the same color as the text that would go on top of it (or at least very close to it).
One possible way of doing it could be to change the Header background color setting to #2D9AC3 (in Apperance > Themes > Custom Totara), but this would change the background color of the footer and header as well (and this may not be what you would desire).
Kind Regards,
Brian