No, nothing that *directly* prohibits it, but the conversations I've had with folks at Microsoft have made it fairly clear that as far as their concerned, importing constitutes making a derivative work.
This has lead me to the conclusion that a GPL program that imports (ie. depends on) something from the .Net environment that is under a more restrictive license (and there is plenty of the .NET code that is) would not be legal to distribute.
So, while it's true that a GPL-licensed program written in generic python would be perfectly legal to distribute and run on IronPython, anything that was written to take advantage of .Net's features (which would only be accomplished by importing other MS code) would almost certainly *not* be legal to distribute under the GPL.
So, no GPL software written specifically for IronPython.