I did a fresh install of a build environment on a new computer, but kept getting configure complaints saying that my SDK version was too low - yet I had Windows 7 SDK loaded. (Visual Studio 2008 SP1, compiling comm-central 1.9.2, running 64 bit Windows 7 Home Premium with MozillaBuild 1.5.1) I managed to get it working with the following fix: in configure.in (which appears in both / and /mozilla), I had to replace references to "winsdkver" to the properly capitalized "WinSDKVer". Only when I did that did this check: AC_CHECK_HEADERS([WinSDKVer.h]) properly find the file.
The Windows filesystem isn't case sensitive, so this really ought not to matter.
"this really ought not to matter" - true. I documented this issue and fix just in case others have the same issue. But it might just be some sort of weird startup glitch for my particular install. That's why I left the status Unconfirmed.