when a tax return comes through that doesn't gel with estimates, or when the top up is going to be huge (as lulu mentioned) it gets diverted to the manual intervention team who go through and check everything to make sure you're not overpaid. this team are specialists, and will get your record checked as soon as they can. there are only two small teams Australia wide. there is no processing timeframe for anything referred to Manual Intervention - they get to it in order of it arriving in the queue. there are no ways to get this pushed through any quicker than it is going to be done. i know only about 3 months ago, they processed 17000 activities in 17 days!

sorry to disappoint you, but all you can do is wait it out. i would suggest contacting ATO and making a payment arrangement for your partners tax (they let you pay it off) and then make the lump sum payment when it arrives