There is a new setting in 6.6 that changes the behaviour of languageEmbedding=never in the linkManager code:
LANGUAGES ALWAYS STRIP LANGUAGE
This setting specifies if the StripLanguage processor in the <preprocessRequest> pipeline will parse and remove languages from
the URL, even when the languageEmbedding attribute of the linkProvider is set to "never". You should only change this setting
to "false" if the default behavior causes problems in your solution.
Default value: true
<setting name="Languages.AlwaysStripLanguage" value="false"/>
This was causing issues post upgrade since we relied on the presence of /en to define different site entries.