[Sony Ericsson Xperia Mini, Mini Pro, Xperia Pro, A] Ticklefish:
You've got your clock with android:layout_height="wrap_content" and android:layout_centerVertical="true".

But your date has android:layout_height="fill_parent" and no layout_center.

You need to change either the clock or the date to have the same attributes as the date or the clock. So...

<?xml version="1.0" encoding="utf-8"?>
<LinearLayout android:gravity="center_vertical" android:orientation="horizontal" android:id="@id/header" android:background="@drawable/indi_noti_settings_bg" android:layout_width="fill_parent" android:layout_height="@dimen/notification_panel_header_height" android:baselineAligned="false"
xmlns:android="http://schemas.android.com/apk/res/android"
xmlns:systemui="http://schemas.android.com/apk/res/com.android.systemui">
<RelativeLayout android:enabled="false" android:id="@id/datetime" android:background="@drawable/indi_noti_datetime_bg" android:layout_width="wrap_content" android:layout_height="wrap_content" android:layout_marginLeft="8.0dip">
<com.android.systemui.statusbar.policy.Clock android:textAppearance="@style/TextAppearance.StatusBar.Expanded.Clock" android:id="@id/clock" android:layout_width="wrap_content" android:layout_height="wrap_content" android:layout_marginRight="8.0dip" android:singleLine="true" android:layout_centerVertical="true" />
<com.android.systemui.statusbar.policy.DateView android:textAppearance="@style/TextAppearance.StatusBar.Expanded.Date" android:gravity="left|center" android:id="@id/date" android:layout_width="wrap_content" android:layout_height="wrap_content" android:layout_centerVertical="true" android:layout_marginLeft="2.0dip" android:layout_marginRight="2.0dip" android:maxLines="2" android:singleLine="false" android:layout_toRightOf="@id/clock" />
</RelativeLayout>
<Space android:layout_width="60.0dip" android:layout_height="0.0dip" android:layout_weight="1.0" />
<TextView android:textSize="11.0dip" android:textStyle="bold" android:textColor="#ff00a040" android:layout_gravity="center_vertical" android:id="@id/header_debug_info" android:background="@drawable/indi_noti_settings_bg" android:padding="2.0dip" android:visibility="invisible" android:layout_width="0.0dip" android:layout_height="wrap_content" android:fontFamily="sans-serif-condensed" />
<FrameLayout android:id="@id/settings_button_holder" android:layout_width="@dimen/notification_panel_header_height" android:layout_height="@dimen/notification_panel_header_height" android:layout_marginLeft="12.0dip" android:layout_marginRight="11.329987dip">
<ImageView android:id="@id/settings_button" android:background="@drawable/indi_noti_settings_bg" android:layout_width="@dimen/notification_panel_header_height" android:layout_height="@dimen/notification_panel_header_height" android:src="@drawable/ic_notify_time_set" android:scaleType="center" android:contentDescription="@string/accessibility_system_settings_button" />
<ImageView android:id="@id/notification_button" android:background="@drawable/indi_noti_settings_bg" android:visibility="gone" android:layout_width="@dimen/notification_panel_header_height" android:layout_height="@dimen/notification_panel_header_height" android:src="@drawable/ic_notify_time_set" android:scaleType="center" android:contentDescription="@string/accessibility_notifications_button" />
</FrameLayout>
</LinearLayout>

This should ensure that the middle of the clock and the middle of the date are on the same line..