Hi Raul, thanks for your message. I think you make a really valid point about the 'conflict of interest'. It would also explain their current behaviour. I have an appointment with another immigration agent tomorrow, hopefully I can get advice on what to do next.
I mixed up the dates re the skills assessment. My partner had his skills assessed in September, visa was lodged end of Nov, and medicals and police checks were submitted in January/February.
As for the 485- my student visa expired in March this year. My thesis is currently under examination and due to be completed within the next 2 weeks, graduation in December. This is a normal time frame for PhDs, hence we are often employed from the moment we submit the thesis (rather than after graduation). I will look into this though, thanks for the tip. The University also said they would sponsor me (although I need to look into the type of visa/what changes were made to the conventional 457). I have been employed with them since February this year (as a project coordinator for an international phd program as well as a research officer/scientist).
Thanks again everyone for your insights, very helpful and much appreciated.