I recently did a complete reinstall of Windows 7, installed all updates, and reinstalled all of my programs, including MikTeX using the 2.9 64-bit version. I ran a XeLaTeX document I had created and successfully run before, in order to re-download and autoinstall most of my packages. This went well, except for polyglossia.sty and gloss-english.ldf, both parts of the polyglossia package; MikTeX prompts popped up (I had set the autoinstall on "ask me" at install) twice for the first file and three times for the second, before moving on and generating the document anyway. The same thing would happen with those two every time I ran the document; I tried changing the autoinstall download from "random" to, eventually, a dozen or so repositories with no better luck. I looked in the directory cited in the autoinstall prompt, and still no polyglossia directory.
Thinking perhaps it was a glich in the 64-bit version of MikTeX, I uninstalled it--successfully except that Windows was for some reason unable to remove the empty MikTeX 2.9 directory from Program Files (86)--I removed it myself, but had to assert administrator privilege to do so. I then ran CCleaner on the Windows registry; there were fixes to be made, but none that appeared to have anything to do with MikTeX. I then downloaded the 32-bit version and installed it, but everything just went as before. And I don't even want to think about the manual download-and-install fiasco that I tried next; it seems you can't get polyglossia.sty to extract from polyglossia.dtx without polyglossia.sty installed first.
Then it occurred to me to look in ALL of my C:\Program Files (x86)\MikTeX 2.9\tex subdirectories, not just the xelatex subdirectory where MikTeX was looking for them, and lo and behold, there polyglossia was... in the latex subdirectory. For all I know, MikTeX was fetching it and putting it there every single time I clicked the go-get-it button. So the question becomes: do I either tell MikTeX where to put it (and how), or where it should be looking for it, (and again, how)? Or should I just move the polyglossia directory to C:\Program Files (x86)\MikTeX 2.9\tex\xelatex with a simple cut-and-paste and be done with it?