Master slides and fonts changing

I am a new user with better than average experience with Powerpoint & several other programs but I am FAST getting frustrated here. I calculated all the pixel sizes based on a common 75DPI screen (based on audience knowledge) and set up my story size to mimic the PPT I was importing (which I stripped of some intricate animation sequences before importing - just leaving the basic content). Theoretically, the content of the imported slides should have "fit". But it didn't transfer well - fonts, layouts, etc. completely messed up. I went back and reset all my masters to smaller fonts after reading a posting that the font sizes don't seem to transfer the same. I saved the file yet the master settings changed and once again I do not have consistent font sizes in my layouts. I gave up on the idea of using the imported slides and am reconstructing each slide but even when applying the new master layouts I am not getting consistency.  I just went back into the master templates and found all the settings I fixed last night and saved are gone. What is UP with this?  I quickly figured out how to build layers, triggers, etc. so having issues with the basics is just annoying. 

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