I've been working with WP eCommerce for over 5 years and "ALL"of your are correct...the latest upgrade of the plugin has virtually shut down a lot of websites.
1. Use the previous version as all the bugs have been removed from that version and it works great with every theme and has no conflict with any plugins any longer.
2. Never, and I mean never upgrade a plugin for at least 3 to 6 months as plugin developers sometimes cannot possibly create the perfect plugin the first time out and I have found that waiting 3 to 6 months is always a safe bet.
3. Always, and I mean always keep a backup of four components of your website....a. Core files, b. MySql Database, c. Theme files which should always include your custom CSS php file as well..and d. XML export file of your website by using the export function.
I have wp ecommerce on 5 of my personal websites and I've created over 20 WP ecommerce sites in the past six months and none of my sites or their sites are experiencing any of these issues.
This is free advice that comes from 10 years of designing websites and plugins...if you need any other help besides what I have posted here. I don't work for free.
Thanks again, Party on