Try this. I just reordered stuff so it stops the timers first thing in the functions, and enables the other one at the end.
Code:
Private Sub Timer1_Tick(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles Timer1.Tick
Timer1.Stop()
Cursor.Position = New Point(Form1.X.Text, Form1.Y.Text)
MyMethod()
Timer2.Start()
End Sub
'part 2
Private Sub Timer2_Tick(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles Timer1.Tick
Timer2.Stop()
Cursor.Position = New Point(Form2.X.Text, Form2.Y.Text)
MyMethod()
Timer1.Start()