Scott - agree that it would be helpful to get an email notifying for updates on these posts. I had this topic saved as an RSS feed - but the last entry to this topic I received a feed for was in January! For some reason, the feed has just stopped working, so I had no idea this discussion was happening.
The following won't troubleshoot anything but I do hope that WPEC's developers take this to heart:
I am very, very happy to see that this issue is being taken seriously finally. I brought this issue to this forum for a client's site as mentioned in the first post. This issue nearly cost me that client and really strained the relationship, as I was the one who heartily ensured that WPEC was the definite way to go for her store. The day after we launched the store was when we discovered that her site traffic tanked - badly - and discovered the search engine indexing fiasco. Unfortunately, once Google penalizes you, simply turning off the offending plugin doesn't fix it. The damage was done.
Not only did she insist (after literally dozens and dozens of hours of me trying to troubleshoot this) that I remove the cart, but as I said I nearly lost the client. Understandably so, as for her, her Page Rank and Google indexing are everything. It took MONTHS for Google to resume indexing the way it had before we installed the cart, and some of her pages still are not indexing properly.
Two clients since then with sites that rely on their traffic and indexing requested using this shopping cart and I HATED having to tell them I can't recommend it.
I did relent and installed the cart on a third client site - however, it is using the Crafty Cart theme so I hoped that all would work well. It does indeed seem to be working fine. I did NOTHING different on this client's site than on my other client's - other than my initial client was using a non-WPEC theme.
I really, really would like to be able to recommend and use this cart, but my business reputation is on the line. Scott, I truly hope that you can get this worked out, and (assuming my RSS feed keeps working) I will follow the progress. You said it best - "urgent" isn't even the word, "catastrophic" is.
Really hoping the problem gets isolated and fixed in a future version. So much of WPEC is amazing, but a little thing like this ruins all the fun.