As reported by Mark Hatle, the values of varflags do not currently get included in the sstate checksums. Ideally they should influence the checksum of the variable they are attached to. This will also neatly solve the issue of the SRC_URI checksums (which can be specified as varflags on SRC_URI) changing to match a change upstream without any other change to the recipe.
Merged to master in the following commits: http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=534f31903b98de9298c69f4de4d6cd1c51d394d6 http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=3e9f270a4766becac28261e61338cf336fdf477e