I have run into this in the confocal facility I run.  People have 
brought samples that they have prepped without first consulting me 
and we have all sorts of strange results.  PE is not a stain of 
choice for fluorescence microscopy.  It is very popular with the flow 
cytometry folks where its rapid bleaching is not an issue, nor 
apparently is its excitation by multiple wavelengths.  I would 
recommend almost any of the other dyes that excite around 560 in 
preference to PE.  You will also get a stronger (enhanced) signal if 
you use your Cd31 as a primary Ab then tag that with a fluorescent 
secondary Ab, although you may have specific reasons for not wanting 
to do so.
Try TRITC, Texas Red, Alexa 546, CY3.  They will all fluoresce red 
and will allow your FITC double stain.
Lee
-- 
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy Core Facility
Manager, Optical Microscopy Core Facility
Joan & Sanford I. Weill Medical College
of Cornell University
voice  (212)746-6146
fax (212)746-8175