How to find which templates are affecting a display? spending hours dealing with form_alter , finally realized that a tpl.php file is overriding the output !!!

now the question is 


  what are the ways to understand which template files(or functions) are affecting a display so they can be customized ?
First, you can easily debug everything with Devel module. Another trick that I use to inspect what tpl is generating a particular element is by adding $conf['theme_debug'] = TRUE; in settings.php. After adding that refresh your page (or clear your cache first) then use inspect element. The tpl should be visible now in the HTML source. See the screenshot below.



Here is a blog that describe on how to theme a field.

Hoe that helps.