I am thinking that you have chosen font sizes or styles that are not converting well in Presenter. Try a "standard" size (i.e. if you have a 23 pt. font, try 24 or 20) or a standard type font (like arial or something generic). You may try saving the file as a .ppt if it is a .pptx as there are some known issues with .pptx format, some related to fonts. This page with documentation about Presenter may help: http://www.adobe.com/support/presenter/?promoid=DNRQX
If David Yun sees this post, he might be able to direct us to a kb article that covered font issues, which I have been unable to find. David has done a nice job keeping track of the particular issues.
Hope this helps.