Things like scripts need to be edited to prevent them changing the second account. This is not always an easy task for an experienced user (or some coders for that matter).
All settings of Messenger Plus! Live are "global" which means they apply to all users of the program. Unfortunately, this means that you must use the same settings across all open Windows Live Messenger clients.
I personally believe it would be a good idea to create a "Profiles" option within messenger plus that can be associated to a specific user account. Obviously some settings would remain global no matter what (such as poligamy... You can't have two Windows Live Messengers open if poligamy gets disabled
).
I may have to put the idea in the suggestions thread somewhere (if I can find it again)
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