If you've cut aluminium before, is something mechanically loose?
What feeds, speeds, tool dia, tool material, tool coating, no flutes, depth of cut, material thickness, material grade .
What spindle size (w/kW).
The 6040 is not very ridgid.... depending upon its design a lot of the load is placed upon the leadscrew bearing(s) which can be very cheap Chinese kfl000 (I think from memory) pillow block bearings which have two grub screws....and the metal can be of questionable brittleness ... but it does depend on the 6040 ...
My personal experience with a 6040 was that it would be great for PCBs, wood, but lacks rigidity for aluminium... also it depends on your cutter, I went with onsrud o - flute cutters which cut well but needed really good chip clearance (continuous compressed air) and cutting fluid (wd40 in my case), and dispite having bigger steppers than yours (4.2a) and a higher power supply (50v ac, 850w, my drives are ac leadshine am882h) my feedspeed with 1605 ballscrews was not good under cutting application and the ridgidity was lacking (hence am pulling my finger out to convert my emco fb2 mill to cnc..., but have been looking for a more ridgid xyz table as I like the cutting bed size, but other than open designs c-beam cannot seem to see anything that's rated for aluminium)
This is just one person's limited experience of using a 6040 frame, and I do use a makita router (rt0700cx4+ Elaire corp collets) with it with a superpid2 speed controller .... PCBs great... wood great... aluminium... borderline... (note my steppers plus drives are probably well oversized... but I use the same size on my 4'x4' 40a pmx plasma htd direct belt drive (20T/5mHTDx20w) custom 2"x2" box frame with roller bearing setup with very very high acceleration and rapid speeds and this allows me to share the same pc + driver and controller box between lathe, mills and plasma. I use to use an ess smooth stepper but have moved on to a uc300eth with uccnc, but may come back to the ess + mach4 licence if warp9 ever sort out the mach4 plasma plugin functionality with m62/m63 as I liked running the ess + m4 with the 6040 mill as the tuned drives seemed to run quieter than the ess with mach3