We have written a MathFlow Equation Composer (EQC) plugin for APP, and yes, we have encountered the same behaviour. The EPS files generated by EQC do not contain embedded previews, so will not show up in APP. However, when you print to PDF the EPS equations will display. If you add previews (as dschenken suggest) then you will see the EPS files in APP, but be aware the EPS file size will be larger.
Another thing to be aware of is that MathFlow EPS also do not contain embedded fonts. This means all fonts must be supplied by the system. APP handles this as follows: during PDF output the EPS files are processed by the PStill component embedded within APP. PStill translates the EPS to PDF. However, PStill does not use Windows fonts, instead you need to convert the fonts to PStill format. You need to use instfonts.exe utility to add any fonts that may be referenced by the EPS, such as Euclid and the other MathFlow fonts.