Ah, excellent. Glad to have been of assistance.
I've done a bit more digging, and have finally figured out what the problem is. The PDF files produced by the Max 2's 'export' function turn handwritten notes into annotations of the type 'polyline', but do not set the 'print' flag for the annotation. According to the PDF specification, annotations will not print unless the flag is set to true. Fortunately, this can be done in Acrobat Pro by running the following in the javascript console:
Code:
var annots = this.getAnnots()
for (var i = 0; i < annots.length; i++)
annots[i].setProps({print: true});
The advantage this method has is that it does exactly what is necessary to fix the precise problem, and does not require you to flatten the PDF.
In Linux, it should be possible to achieve the same result with
pdfedit, but unfortunately I don't know its scripting language so I can't help further. However, this only matters if for some reason you need to avoid flattening the PDF. If all you want to do is to print and don't care about flattening, just use
gs as discussed above.