The type I am referring to is the words "What to do next" above.
On the left is what they look like in the native InDesign CS5 file they were created in. This is how I would like them to appear.
On the right is how they appear when I try to save the brochue as a .pdf.
My question is how can I get the words "What to do Next" to appear the same in the .pdf as they do in the native InDesign file?
Thanks for your help!
Effects are usually using some type of blending mode - you should preview your InDesign file using View>Overprint Preview
That will show you what they look like when they blend with the background.
Try using the PDF/X-4 preset.