Ok, I think I'm getting closer to understanding this... I probably knew what you were talking about back when we played at first, and then forgot sometime in the interim.
Let's take, say... an Ogre Factotum 2. Strange combination, sure, but that's beside the point...
The Ogre Factotum 2 has the full class abilities of a Factotum 4, and basically just reads the Spell Level, Inspiration Points, and Special columns as if he were such, although he calculates his HP, BAB, etc. as a level 4 giant/level 2 factotum.
Something a little more practical, say a Psion 4/Factotum 2 has an ML of 5, 25 power points, and can theoretically learn 3rd-level powers, but wouldn't actually know any if he took these classes in this order. Also, he would only have the class features of a level 2 Factotum, but if he took a 3rd level, then maybe he'd gain his 4th inspiration point (as a Factotum 5 would)?