This has been fixed in Autopano Video Pro 1.5 Final.
I've noticed that upon changing the frame resolution for renders (and clicking OK or Apply), then when opening the render settings again, notice how the max resolution value has been adjusted to match. So the "maximum size allowed by source" is changing, which is confusing since that should stay constant based on the raw source footage. This experience is consistent in any project, regardless of the projection selected.
It can only then be reset to the true max resolution after going into APG and toggling the projection type or adjusting the fisheye FOV.