I consulted for a defence contractor several years ago that was involved with welding aluminum. The wax did prove to be troublesome if it wasn't completely removed prior to welding.

I suspect you are correct in saying the vapor degreaser removed the wax prior to welding. We didn't have a vapor degreaser and the wax was a nightmare. We had a devil of a time removing it completely. We ended up prohibiting the use of waxes for joint preparation or for the excavation of welds to be repaired. We did use wax for finishing welds. However, when porosity was encountered while finishing welds, and they needed to be repaired, great pains were taken to remove the wax residue before rewelding.

I recently consulted for another fabrication house that works with aluminum exclusively. They consistently produce some of the best aluminum welds I've seen. They use routers with carbide tools to prepare the weld joints. No wax is permitted except when finishing (i.e., grind the welds with "soft" pads and sand paper) completed welds and to "lube" the band saw blades when cutting material to length.

I observed the welders wetting the carbide cutting tools with isopropyl alcohol to minimize "loading" by the aluminum. It is not as effective as the wax, but it leaves no residue on the aluminum. The welders were religious about flushing their tools with isopropyl alcohol before every use to remove all soils, grease, etc., as well as to help prevent "loading" the cutting edges. They also flushed the joint with isoproply before welding (not simply wiping the joint with a saturated rag). The welders were doing everything I "trained" the welders to do several years earlier at the previous company I mentioned.

If you really wanted to tick-off the welders, just use the wax with their joint preparation cutters and stand back to watch the fire works. The welders would all but jump down the "finisher's" throat if they caught them using their tools with wax. 

Best regards - Al

For weld bevel preparation, on a new plate, you can use an ordinary skill saw with a carbide tipped blade.  For groove preparation on a repair, or to back gouge, use a grinding  disc or a carbide burr (rotary file).  I recommend using a 2 or 3 flute carbide burr when grinding aluminum, because it doesn't load up like the rotary files used for steel.  Use K-1 Kerosine as a lubricant (just dip the burr into it every few seconds, do  not pour it into the groove).  For grinding with an abrasive disc, use the ordinary Aluminum Oxide discs for fast removal, and don't worry about the disc loading up (wear face and eye protection).  Don't use wax, - you cannot easily remove it from the metal, unless you have a special vapor degreaser, or a good hot flame. After getting the groove prepped with an Aluminum Oxide disc, follow it up with the Carbide Burr to remove the smear and the oxide grit.