1.Create a form let say 50000 Customer Test based on table 18 with some fields.
2. Now after saving it go to File->Export & save this form as Forms.xml in (I have put it on the same folder of where this Microsoft.Dynamics.Nav.Tools.FormTransformation.exe exist)
3. Now i run this Microsoft.Dynamics.Nav.Tools.FormTransformation.exe
this will only create other Transformation.log & TransformationLog.xml file only.
This will not created the pages.xml in the same folder.
you seem to be missing some steps. You should probably try following some of the online documentation available on MSDN or the NAV 2009 online help. Try this link for starters: http://msdn.microsoft.com/en-us/library/dd301209.aspx