I have layout structure:
<LinearLayout
xmlns:android="http://schemas.android.com/apk/res/android"
android:layout_width="fill_parent"
android:layout_height="fill_parent"
android:orientation="vertical" >
<com.google.ads.AdView
android:layout_width="fill_parent"
android:layout_height="wrap_content"
ads:adSize="BANNER"
/>
<LinearLayout style="@style/TitleBar"
android:layout_width="fill_parent"
android:layout_height="45dip"
// title bar
</LinearLayout>
<RelativeLayout
android:layout_width="fill_parent"
android:layout_height="fill_parent"
android:orientation="vertical"
// main layout with all needed elements and background!" >
</RelativeLayout>
</LinearLayout>
Everything look fine, until my AdMob disappered. Then I can see empty black region with admob size.
UPDATE: my screen shot:

normally I cas see here ad block, but when I get onFailedToReceiveAd(Ad request successful, but no ad returned due to lack of ad inventory.) ad disappers and my layout not fill all screen.
What you describe looks weird…
The reason I believed caused an ad to disappear was in case an ad is refreshed and then no ad is served due to lack of ad on AdMob side.
But from my own test, once an ad is loaded, if a subsequent ad refresh fails, the previous ad stays displayed, I haven’t seen ads ‘disappear’.
Maybe you could look at logcat and see if you get any errors there.
Here is some code I used to test Ad Request delivery/failure on my own app.
In case the blanks appears after an Ad fails loading, I suppose you could put some code inside the onFailedToReceiveAd to resize the AdView