I know this thread is old, but I was experiencing a similar issue and have resolved it.
First off, with Autodesk products, I found the admin install utility would create huge packages with tons of tiny files. Configuration Manager doesn't do very well with these, so I ultimately wound up compressing them using 7-zip and writing a script that would decompress the files, run the install, and delete the extracted copy. It takes longer to do the install, but most Autodesk products compress to about 50% of their original size, so the software download is much faster. This especially helps our VPN users who install software when they are out of the office.
I also had the "Package 'XXXXXXXX' is found in active queue, will try it later" message in distmgr.log. When I used the Distribution Point Job Queue Manager tool that is part of the 2012 R2 toolkit package, I found that there were no jobs in the queue, but I kept getting these messages in the distmgr.log file. I finally just restarted the sms executive service and distmgr started processing jobs normally.
Hope that helps anyone else who finds this thread.
--Russel