rosrun ambiguities after migrating to hydro

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I'm currently migrating from fuerte to hydro (on an Ubuntu 12.04).
In a first step, I kept all my old packages dry and managed to build them in hydro.
Running the system on the other hand seems to be more complicated.
I'm using my own, slightly altered versions of some popular packages such as move_base.
To tell whether to use the original move_base or my version I used to change the include order in ROS_PACKAGE_PATH, which worked fine.

The hydro version of rosrun, however, reports an ambiguity:

[rosrun] You have chosen a non-unique executable, please pick one of the following:
1) /opt/ros/hydro/lib/move_base/move_base
2) /path/to/my/version/of/move_base/bin/move_base
#?

If I try to call move_base from roslaunch, it will choose option 1 per default.

I've got the same problem with move_base plugins. Once I tell rosrun to load my version of move_base, it will still load move_base plugins from hydro.

Is there a way to tell hydro to load packages from ROS_PACKAGE_PATH per default?

echo $ROS_PACKAGE_PATH returns:
/home/incubed/robotics/incubed-ros-pkg:/opt/ros/hydro/share:/opt/ros/hydro/stacks