Referring to this topic http://wordpress.org/support/topic/from-email-address-wont-change-when-sending-html-email I would like to repost my previous post as it seems that nobody looks in the topic, already marked as [resolved]:
I don't see this problem resolved in version 3.5, maybe there is a conflict with other plugins than S2Member, which I don't use.
I'm especially using the following plugins with mail functions in my installation:
SB Welcome Email Editor v3.5
ALO EasyMail Newsletter v2.4.14
Contact Form 7 v.3.3.3
As long as I have SB Welcome Email Editor activated, the latter two will have a generic hosting email adress as "from" instead of the specific ones defined in the plugins.
Therefore I had to deactivate SB Welcome Email Editor for the time being.
[ Second edit: carry on, you've opened your own topic which is the right thing for you to do. ]