To lock in a font try to convert your EPS to outlines in Illustrator (if if you have Illustrator and willing to do that). Also, make sure that the desired font is installed on your system and works in AE itself. What kind of font is it?
If you are seeing letters dropping out, I suspect the type may be too small for extrusion. Again, in Illustrator, if possible, increase the font size or make it bold. Some curves are hard to extrude if they are too tight or tiny.