My understanding was that he used Nuendo... but really all those programs like Cakewalk and even Pro Tools are pretty much interchangeable - they all do the same thing, just a little differently in how they are setup/presented.
I get the impression Symphony X actually tries to keep their gear quiet... I'm not quite sure why, but they never seem to be all that forthcoming about too many studio specifics. Could be that they just cobble things together and don't really pay too much attention (which I do sometimes). But in one of those pics you can see 4 different guitar amp heads (2 line 6, a marshall, and an Engl), and MJR pretty much only ever mentions the Vetta. Now, just cause they are THERE doesn't mean they use em all... but I would bet a lot of their studio stuff comes from tinkering around with a lot of combos (and then probably not really even recalling what the hell they did).
Frustrating because I would gladly spend a whole day discussing the recording techniques on V if someone cared to have that discourse.