Amazing… I don’t believe I experience this slow behaviour on Windows or Mac. So something fishy must be going on which causes this slow speed ;-(
Stacking 40 Canon 6D frames only takes about 21 minutes on my Windows 7 i7 930 quad core, (which is almost 7 years old).
Are you using the 4GB version on the machine with 8GB mem?
Are you running the stack with or without oulier rejection? If you are, turn it off and check if that has some influence? Do you know which part of 3)Calibrate to 6)Integrate has the longest duration?
Possibly the platform in which APP runs has a problem on your Linux Mint system, which I am unaware of at the moment. Maybe we could schedule a remote desktop/teamviewer session next week so I can have a look at how APP behaves on your system(s)?
Mabula