I have a multisite install that I am working on for a school district running on a:
-Windows 2008 R2 server
Everything is finally going along fine, took a while to get the re-write rules to work, but once I got it working I installed my general stack of plugins, and all of a sudden every ajax request is throwing a 500 internal error.
To further obscure the problem, this only happens on daughter sites, the primary site has no issues at all. Everything else loads fine except ajax requests. I tried directly loading the admin-adax.php file through the daughter site URL and it properly sends a 0, so the re-write rules are working properly.
Next, I deactivate all plugins. After a process of elimination, I found that both of the Plugins from Yoast are causing the issue, first I discovered his SEO plugin causing the issue, but after further testing, I found that his Google Analytics plugin is doing the same thing. With both the plugins deactivated the network sites work fine and ajax requests are not a problem. No other plugins in my stack are causing any problem after re-activating them.
I finally took it one step further and tried activating the plugins on a per-site basis rather than network activating them. Doing it this way, they both actually work fine, no ajax errors. This is good because I think Yoast writes some great plugins and I would be quite disappointed if I was unable to use them on my client sites. However, I think this is both useful info for the community, and hopefully useful for Yoast. It is a very obscure install, but it is a problem. If I am misunderstanding anything, I would most heartily welcome feedback.