You need to clarify somewhat what you're experiancing when you say it "does not sound right". There have been people reporting some trouble when it comes to the alt tunings (I don't know what Zap is thinking when he says he hasn't seen people posting about it).  Some of them are definitely software glitches that can be fixed with a flash, but there's a couple that can occur even when everything is working perfectly:

1) Simultaneous mags + model

This is one a few people have accidently run into when using the HD500. They'll manage to set things up in the patch so that they're including inputs from both the magnetic pickups and Variax model at the same time.  And that's fine... except once you get into alternate tunings. Then you end up with the mags input in standard tuning and the model input in the alt tuning.

However, since you're noticing it on a specific string, it's more likely that it could be the following

2) Sympathetic resonance

I've written about this a couple times, most recently here: http://line6.com/support/message/408008#408008. There's no way around this - unless Line 6 work some mighty impressive voodoo - so the only way handle it is to make sure to employ proper string muting with your palm/fingers when you play (which is good to be doing anyway).