Yes, if you do a foundation in STPM / A Levels etc., it will be generally recognised by all private universities. But if you do a particular private college's foundation programme, it may not be recognised by others. I guess this is to prevent students from hopping between colleges.
You can check http://www.malaysia-education.com/pre-university.html for a list of the top pre-university programmes, and http://www.malaysia-education.com/diploma.html for diploma programmes.

You don't need super SPM results to get a place in many private colleges. Once you get a place, it's like a fresh start; a second chance - just work hard and smart!