The issue was being caused by
    ::SendMessage(m_hwndSite, WM_NCCALCSIZE, FALSE, XTPToLPARAM(&rc)); being called when the child frame didn't have the WS_DLGFRAME flag in its style (which happens in CXTPCommandBarsFrameHook::RefreshFrameStyle).

I solved the issue by making this:

BOOL CMainFrame::OnWindowArrangeCommand(UINT nCmd)
{
    if (!GetSafeHwnd())
        return FALSE;

    CWnd* pWnd = GetActiveFrame();
    if (pWnd != this)
    {
        CChildFrame* pChildFrame = dynamic_cast<CChildFrame*>(pWnd);
        while (pChildFrame)
        {
            pChildFrame->PrepareForRearrange();
            pChildFrame = dynamic_cast<CChildFrame*>(pChildFrame->GetNextWindow());
        }
    }

    const BOOL bRet = CMDIFrameWnd::OnMDIWindowCmd(nCmd);

    UpdateMDIChildrenTheme();

    return bRet;
}

and

void CChildFrame::PrepareForRearrange()
{
    m_bLockNCPaint++;

    RECT rc = CXTPWindowRect(m_hwndSite);
    ::SendMessage(m_hwndSite, WM_NCCALCSIZE, FALSE, XTPToLPARAM(&rc));

    m_bLockNCPaint--;
    RedrawFrame();
}