I haven't tested this fully, because as you can imagine, our #1 priority was to get our stores processing payments properly again. However, we've seen this across 3 different sites.
We recently added Stream across all our client's sites, excited about the possibilities of it's tracking capabilities, and integration with MainWP's extension to send our client's reports on their sites. We were on the verge of purchasing the extensions to add the WooCommerce tracking to our client's sites that have an eStore.
Then yesterday I realized that on our own estore, no subscriptions had been processed for a couple of weeks. We started looking at possible causes and updated several PHP settings, etc. We also noticed that comment moderation wasn't working. Nor could we trash a subscription (WooCommerce Subscriptions) or an order. Comment moderation appears to work, but upon reloading the comments page in WP admin, nothing had changed. When trying to trash an order or subscription, the URL would change, but the browser would go to a white screen, and going back and refreshing revealed that the action had not taken place.
None of the PHP and other server setting updates helped. I then disabled several non-essential plugins, including Stream. Suddenly, everything worked fine. On reflection, Stream had been installed about the time the subscriptions stopped processing. I enabled all of those recently disabled plugins, except Stream, and everything has continued to work.
I then received emails from a client with an estore, he reported the exact same symptoms. Disabling only Stream fixed all issues on his site. I checked a 3rd estore/WooCommerce site, same sypmtoms, same fix. I remembered that on my personal blog (no WooCommerce/estore) that I'd been unable to properly moderate comments recently, so I checked there, same symptom, same fix. So we've disabled Stream across all sites now, as we can't afford to loose basic functionality, and especially can't have payments on orders and subscriptions not processing.
I assume that if this were a universal problem, you'd have fixed it by now. So I don't know if it's a conflict with another plugin we use, or what. I'd be happy to do what I can to help. We'll certainly be a little gun-shy about re-enabling the plugin, but are excited about it's possibilities and so with proper testing, would like to get back to that point. Here's some basic info to get you started:
Some general server settings we messed around with, but didn't seem to affect this problem:
Web Server Info: Apache/2.2.26 (Unix)
PHP Version: 5.3.3
MySQL Version: 5.5.38
WP Memory Limit: 256 MB
WP Debug Mode: No
WP Language: Default
WP Max Upload Size: 32 MB
PHP Post Max Size: 32 MB
PHP Time Limit: 60
I cross-referenced the plugins running on the WooCommerce sites, and my personal blog (since it has relatively few plugins, but showed the one common symptom), and here's the plugins they have in common that might be conflicting with Stream:
All in One SEO Pack Pro*
iThemes Security (good possibility)
Subscribe to Comments Reloaded
The ones with * next to them are premium plugins, but are GNU so I can get you a copy if you don't have one. As I noted iThemes Security is a good possibility for a possible conflict. I don't have time to test now, but may tomorrow. It may be a matter of changing it's settings to work differently, if it is the one conflicting with stream.