During rootfs generation, opkg is replacing the status file and thus ends up ignoring the bad recommendations that were add on it before installing the packages. This has been tracked down to opkg install as before the first package installation the status file is fine.
Fixed in master in http://git.yoctoproject.org/cgit.cgi/poky/commit/?id=8135963ff2cfac7af69a3e5726837ac469cd9a0e