Quick question, some sites say the guitar is basswood, others mahogany. WHich is it? Or are there two different versions?

It's basswood bodied.. All of the new neck through models are..

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Chaos, panic, and disorder.. My work is done here.

That's odd... How do sites like this get away with it then?

http://www.sweetwater.com/store/detail/SLATTXMG36/

The information is initially provided by Jackson, and more often than not, the first release of new model information is incorrect. Some retailers will go back and correct the issue on their sites, some taking longer than others, and some just don't... Historically, this happens rather often with new Jackson models..

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Chaos, panic, and disorder.. My work is done here.

Gotcha, thanks.

I had asked Jackson about the wood used, and they tell me that it is indeed Mahogany, and that they will have to correct this piece of information across the boards.

But of course, it could be indigenous mahogany from Indonesia, unless someone from Jackson insists on importing wood for building the guitars in that factory in Indonesia, likely to be Samick.

Actually we seem to have a bigger problem.
I'm in the same boat as the OP. I'm thinking of buying one myself..

This website says that it is made of basswood...The new Jackson catalog says it's mahogany. So it's not just some outside random website or anything that is showing this conflict.

Jackson's website is not quite the most accurate source of information, and they keep getting it wrong most of the time, as fans have noticed. A representative said that this is a mistake on the main page and other communication and they will fix it in some time. Maybe now these models will start selling well- it's hard to ignore a mahogany-bodied arch-top Soloist with a Floyd Rose Special (not some LFR) and active EMGs- unless some folks complain about the absence of sharkfins. Over to some user reviews now.

Actually I still think there's more to it than that.
The demo video of the guitar on this site says that it's basswood and I found a youtube vid of that bald dude from Fender demoing the guitar saying that it's basswood as well.

So there's definitely something odd going on I think.

Changing site information is easy. They can't re-shoot the video so easily. Already a few YouTube videos have this apprehension expressed in the comments section.