MODULE_init() question

When developing modules prior to v6,
I was able to override $conf settings using MODULE_init() ...

I was overriding in particular:

$conf['theme_default']
$conf['default_nodes_main']

I have tried to do the same thing with v6,
but the override effect only worked when I had the variables outside of the function..

Now, this may be because the module itself is not complete and I am only
adding bits and pieces as I go on..

But should the init() function work the way it did previously,
or is there some new logic in v6

Thanks