I recently had to set up a PC with similar kit as I have on my Mac. On this PC the OS is Windows 7 64-bit but the browser is IE8 32-bit. This causes jucheck.exe to install (and occasionally update) 32-bit Java. This is unfortunate if you use 64-bit R, because it breaks the rJava package, which in turn breaks the xlsx package, with the practical consequence that you cannot read Excel worksheets into R.

There is a workaround. First, install Oracle's manual download of 64-bit Java. As of this writing, its Windows 7 home will be in C:\Program Files\Java\jre7. You should add this to the %path% environment variable. In addition, the rJava package depends on jvm.dll, and R might be looking for it in the wrong spot. It won't hurt, then, to add this to your %path% as well: C:\Program Files\Java\jre7\bin\server. There's more on this, as usual, on StackOverflow.

As Oracle warns, your manually-installed 64-bit Java will not be automatically updated. That is a problem when security flaws hit Java, but I find being able to read Excel files into R so useful that I'm willing to just live with this risk, though I don't have a good idea how to best manage it. I'll just keep an eye on ArsTechnica for bug news. If anybody has a better way, I'm all ears.