Getting logos to line up properly is one of the hardest things in slide design. I have not been able to come up with a set of rules to do it, every time I need to eye ball things to see whether things somehow look right. Below is an example from the 9xchange web site:

There are a number of (conflicting) inputs:

• The middle of the image file

• The typographical baseline of the text

• The middle of the non-text part of the logo

• Tag lines above or below the brand name

Always fine tune logo pages because any automated adjustment will for sure not get it right.