scene: Missing script links with custom version control

As Unity Pro user, we noticed that with Unity 3.5 and 4.0 series, under the following conditions, the game objects that are previously linked with scripts in a scene (.unity file) will complain that the scripts are missing:

1. when the project assets folder is relocated.

2. when we manage assets with custom version control system, and the assets are checked out into a new location.

3. Someone checked in a scene after local changes.

4. when a project created on Windows is imported to Mac, or the other way around.

We haven't tried Unity Pro's builtin version control feature simply because we lack the resource to do so. This has been a serious problem for us because it means:

1. The scenes are not exactly version-controlled, because we have to manually re-link scripts to every single game objects in a collaborative setup.

2. We have to maintain two copies of the same content for Unity Windows and Unity Mac.

We strongly feel that there must be some misuses on our part here. Does anyone have tips about this?

Thanks a bunch!