One symptom:
The behavior of GOROOT_BOOTSTRAP=$HOME/go1.5-bootstrap ./make.bash and
GOROOT_BOOTSTRAP=$HOME/go1.5-bootstrap/ ./make.bash are vastly different
even though the only difference is just a trailing slash added to GOROOT.
($HOME/go1.5-bootstrap is a Go 1.5 installation)

The first will not rebuild std in $GOROOT_BOOTSTRAP, however, the later will.

An easier repro:

$ goroot=`go env GOROOT`
$ cd $goroot/src; ./make.bash # a fresh build
$ GOROOT=$goroot go build -v ../test/helloworld.go # it only build helloworld.go
$ GOROOT=$goroot/ go build -v ../test/helloworld.go # it will recompile runtime

This behavior suggests that some paths that get included in the buildid hash
are not properly Cleaned.