I have similar issue.
eg, My website has two langauges -> English and Hindi.
Now, English is my default language and very few pages are in Hindi.
My Homepage is available in both English and Hindi.
If a user selects Hindi language, he is directed to Homepage (Hindi). If he hits a link on that page which does not have a Hindi version, he is taken to the default English version of that page, but his language preference is then lost. If he tries to visit homepage after that, he sees English version and not Hindi.
Basically, the plugin somehow destroys the memory of user's language-preference once he reaches a page which is available only in default language.
Has anyone resolved this issue?