How have you implemented your custom tool tips?
WPF standard behaviour for tooltips, even customized ones, is that it appears next to the cursor, as in this example;
<Window x:Class="WpfApplication4.MainWindow"
xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
Title="MainWindow" Height="350" Width="525">
<StackPanel>
<Button Content="A" ToolTip="Simple"></Button>
<Button Content="B">
<Button.ToolTip>
<Grid Width="100" Height="100" Background="DeepPink">
<Label Content="I am not simple"/>
</Grid>
</Button.ToolTip>
</Button>
</StackPanel>
</Window>
Unless your tooltips require some very special treatment, you should be able to do customized versions using that type of construct.
Hope this helps,
Fredrik