There have been several separate things that lead to this message popping up; the pop-up itself is a symptom, not a cause, of another fault; to fix it what I have to do is work back to the root causes.
The most common of the causes (accounting for virtually all of the cases)
was fixed in 2.0.1. The problem for me in fixing the remaining cases was that they are incredibly rare and it would not happen for us in our laboratories to allow me to gather any information on what might lead to them. This has made progress very slow as a result.
I'm confident that I have identified and fixed in the code the root cause of the remaining instance of this popup;
however, there are other problems with the process of upgrading clients from 2.0.1 that are not reliable enough (I'd describe them as more painful in practice than the pop-up itself). So, in order to move forward we have also had to redesign the upgrade procedures to ensure that any fixes we make more widely available go in smoothly.
Changes of this magnitude require a lot of QA work to find regressions and ensure that they don't cause additional problems; that testing and stabilisation process is underway, but by its nature it takes as long as it takes. I can't tell you when it will be done, but we're working on it.