VGA is generated directly by the graphics Hardware, and is supplied on the bar at the end of the connector and basically the four pins around the bar. The adapter used is only an adapter, no signal conversion is performed. VGA working or not working is not particularly meaningful.

What does that listing show when you:
1) connect the display you care about to the port you really want to use (presumably the second DVI).
2) deliberately switch the monitor so that it is accepting input from the port you connected it to
3) Press the ( Detect Displays ) button at the macintosh end.
If the name of the display is not showing up, something is fundamentally wrong with the setup or the secondary channle is not working to accept the display_name and capabilities.
If the name shows up but no picture, it is a simpler problem, possibly a bad adapter or cable.
If the problem follows the adapters or cables or the other Graphics card port, you can isolate it that way.
If the problem does not follow the display or cable or anything except it always fails on the second graphics port, then the DVI portion of the second graphics port is the problem.