Dear Sir,
I am sure your post will help other customers as this topic is on the public area. Up to now we have used modelsim, as well as describing how to simulate the reference design and the steps been working outside of ISE, directly in modelsim. I guess you can see that in the CD document for FMC12x (The constellation description, CD104(ML605_FMC125).pdf, page 7 and above).
We are moving towards ISIM and then we have the simulation running in ISE. This is the case for quite a few firmwares but not yet FMC12x.
Best Regards,
Arnaud