We had a Django 1.5.5 machine working with the 1.3.1 mssql connector with no problems (1.3.1 since when trying 1.4.2rc2 we had a problem with the datetimes in django's log table).
After upgrading Django to 1.6.1, we are unable to create or modify objects via Django's ORM. The most curious thing is that I will create an object and the index autoincrements, but the row is not created (or is created and deleted silently). UPDATE has no effect. DELETE I haven't tried yet. SELECT works fine.
I've tried 1.4.2rc and 1.5a, but they made no difference (with 1.5a at least the datetime problem is not there anymore).
Windows machine, Python 2.7, SQLServer is 2008 (I believe, I'm not sure right now) in a different machine.
If I downgrade Django to 1.5.5 everything starts working again, so I'm not sure if this is really your problem or Django's. Tomorrow I'll try Django 1.6 and see what happens.
Any suggestion I could try to find out what's wrong?.