Thank you for sending the problem file to me. Looking at it in the debugger, I see that the metafile contains 69394 objects. My suspicion is that this number is larger than the largest 16-bit number (65535) and that this is causing a problem in the list class in the Microsoft library code (or perhaps somewhere within Metafile Companion). I do not see any obvious problem in the Metafile Companion code, so I can't come up with a quick fix. So for now, I would have to say that Metafile Companion cannot select all the elements in a file with this many objects.
Just to be clear on the "efficient metafile generation" issue... A metafile generation program can draw a curve with 1000 two-point line segments or it can draw it with one polyline with 1001 points. The first method would generate 1000 objects for a "single" curve. The second method would generate just one object. This is a huge difference to editors such as Metafile Companion. So you might see if the file could be generated more efficiently. Then it could be easily edited in Metafile Companion.
I hope this helps...
Larry