I don't think their change in company structure broke their technology. They've had issues with rebills/subscriptions, email notifications not being sent, IPNs not working, and push notifications firing too many times (just off the top of my head) the past month or so. I would think none of these were connected to Ebay from the start.
I could be wrong but I'm pretty confident PayPal and Ebay have had separate servers, technology, and been pretty much separate entities for a long time. They just had the same board and their accounting was together in terms of reporting to investors.