Two surfaces that had not caught up with the theme
Agent run output (the log block that opens under a run on the Activity page and in the Agent runs panel) was painted a fixed near-black with pale blue text, left over from the interface Pekan used before the redesign. It ignored the theme completely, so it stayed the same cold slab whichever theme you picked, and read especially oddly in the light themes. It now uses the theme's own colours and sits recessed inside the card that contains it, so it reads as an inset well of machine output rather than a foreign block. The two copies of it, which had drifted into slightly different styling, are now one component.
The Windows caption buttons (minimise, maximise, close) are drawn by the operating system rather than by Pekan, so their background has to be handed to Windows explicitly. Pekan was handing over the panel colour, which matches the header beside them in most themes but not in Ember, where the window frame is deliberately darker than the panels inside it. That left a lighter strip in the top-right corner of every Ember window, against the near-black title bar next to it. The seam is gone. The colour used before the window has finished loading was also warmed, so starting the app no longer flashes a cool white strip.
The readability check that guards every built-in theme now covers the log block's text as well, so the pairing cannot quietly drift below the contrast floor in a future palette change, including in any custom theme you build yourself.