StackPanel, by design, does not care about visual space. It aims to take up the smallest amount of space possible. You can leave the innermost StackPanel that wraps the radio buttons in place, but your outer layout containers should be changed to Grid or, as in my example below, DockPanel:
<Window x:Class="Window1"
xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
Title="Window1" Height="445" Width="515">
<DockPanel Name="spDataFlow" Margin="0,45,0,0" >
<DockPanel x:Name="stkPnlDataFlow" VerticalAlignment="Top">
<Grid>
<Grid.ColumnDefinitions>
<ColumnDefinition Width="*" />
</Grid.ColumnDefinitions>
<Grid.RowDefinitions>
<RowDefinition Height="*" />
<RowDefinition Height="Auto" />
</Grid.RowDefinitions>
</Grid>
<StackPanel Grid.Row="1" Background="Red" Margin="20,15,0,0" Orientation="Horizontal" VerticalAlignment="Center" >
<RadioButton Name="rdbtnUploadData" HorizontalAlignment="Left" VerticalAlignment="Center" FontSize="12" Foreground="White" Content="Upload Data" IsEnabled="True" CommandParameter="UploadAll"/>
<RadioButton Name="rdbtnDownloadData" HorizontalAlignment="Left" VerticalAlignment="Center" FontSize="12" Foreground="White" Content="Download Data" Margin="20,0" CommandParameter="DownloadAll"/>
<RadioButton Name="rdbtnUploadSelected" HorizontalAlignment="Left" VerticalAlignment="Center" FontSize="12" Foreground="White" Content="Update Data" Margin="10,0" CommandParameter="UpdateSelected"/>
</StackPanel>
</DockPanel>
</DockPanel>
</Window>