I found the source of another delay when starting apps. I have both English and Japanese keyboard layouts installed, and the English one was modified to put the apostrophe next to the ‘1′ key (like an Amiga keyboard).
For some reason, this started to cause apps to take a moment or two to start. I removed the modified English keyboard, logged out, logged back in again and re-installed it. The delay dissipated.
I investigated the problem a little further and some people report that running “sfc /scannow” fixes it too. The sfc program checks all system files are the original versions, and if they are not it replaces them. It looks like the non-standard keyboard file is causing some kind of delay as Windows checks it over. I read somewhere that Windows will check certain files and programs for compatibility issues by loading them into a special process and seeing if they crash before deciding whether to allow it to be used as-is or with some compatibility hacks. It’s only a guess but I have a feeling it must be something like that.