Hi Vincent, if you have all the data required for the fcs you should be able to do that with the write.FCS() function from flowCore package in R/Bioconductor. It is still experimental but should work out of the box.
Windows should not be a major drawback since R has been ported to win and mac very successfully.
Furthermore, you can perform all your FC analyses with it, and after trying it you provably won't go back into commercial software anymore.
Best, Daniel
PS. Read the vignettes and take your time to learn.