I have never seen anything like that before, maybe some PHP module or even an Apache module.
I would start with a basic test not using Yii just simple PHP trying to reproduce the problem in different ways trying to rule out different components.
Then run it with some get variables eg: /get_test.php?some=123&test=not_yii
If that all looks good. Then move your test into the the top of index.php before yii is run. Then move it after yii is run. If it does not work at the top of the index file then it could be some sort of url rewrite problem. you could also try removing your .htaccess file and testing and then putting it back and see how things change.
I would also compare setup EG: phpinfo vs phpinfo and $_SERVER variables for unexpected differences.
When I changed urlFormat to "get" instead of "path" everything was working fine.
On the forum I found alot of linux problems because of case sensitivity so I changed the name of the controler in the rules to mailingSubscription because the controller name is MailingSubscriptionController.php
But I still don’t know why the $_GET variable got messed up. Maybe it’s a bug in the framework.