Enabled modules get disabled

Is there are any related module which manage modules in safety way?
Like, show me only disabled modules which I want to enable.
When I've got lot of the modules, it's a nightmare to enable only one module.

The same, all my modules has been disabled by them self, but this one I've got this message after enabling some module:

Disabled messaging sending method Mime Mail and replaced by
Disabled messaging sending method PHPMailer and replaced by
Disabled messaging sending method Privatemsg and replaced by

It's a critical bug, which reseting enabled modules no related at all with that I'm enabling.

Disabled messaging sending method Mime Mail and replaced by
Disabled messaging sending method Privatemsg and replaced by
Filter PHP has been disabled.

I lost few days of configuration of those modules and now is mess up.
Temporary assigning to Drupal until I'll find which module is doing this messing (because I need to start from somewhere).
Because in my opinion I should able to confirm if something want to disable any of my module during installation process.

I'm looking for solution described here: http://drupal.org/node/364900

Probably it's Messaging related, because each time I've got this message.

1.
Is this module somehow disabling any of contributed modules depending on filter or something?

What this function do?

/**
 * Find a suitable replacement for a sending method
 */
function messaging_update_method_replace($method) { 
...

2. If it's replacing something with something, why the second argument is empty?
What does it mean?

I've got around 200 of them, so I can't specify exactly one.
I'm enabling couple of random modules in the same time (specially when they have some dependencies), and then even I'm not touching Messaging (which is enabled), I've got message from Messaging module that I've sent it before (it's weird if it's executed even I didn't touch Messaging module).
After that most of the basic modules are disabled.
One of which has been disabled were: Google Analytics, Job Posting, Aggregator, Panels, Activity, abuse, Ad, Notify, Workflow, Smileys, Invite, Email (some other CCK related) and many more.
Later I'll try to to test it again on my local environment to reproduce it.

I thought you will know why this message appear when I'm enabling other modules (not touching Messaging module).
Ok, I'll check it more deeply.

I think it could happen because of partially disabled cache (menu and form tables - #321154: can I disable cache_menu? how?).
http://drupal.org/node/93779#comment-1254794
But it just assumption, because it's difficult to debug 7GB of logs;)

@brianbrown:
Do you have some custom cache modules or modified some core files related to cache? If yes, try to disable them.