Sadly I must report that I am still seeing performance issues even with the new, separate, proxy.
Initial results were promising, when running a single job it would often have throughput at or over 100MB/s. Unfortunately, as soon as a second job that uses that repository kicks off, performance suffers greatly. Before all this, we could run 2 server jobs at once and, though each had only about half the throughput they normally would, they would still run smoothly. Now, whenever I attempt to run two at once, performance for both jobs drops to <1MB/s.
This on its own would almost be tolerable, however I am now seeing that longer running jobs are showing the same issue as before, even when they are the only job running:
Note how the job seems to begin with promising performance, only to later become tragically slow. Veeam keeps blaming the network, which makes no sense. If Veeam would better report what the actual problem is I suspect I'd be much closer to remedying it. Given the amount of time I have spent on this issue, the impact it is having on our ability to backup production data, and the relative lack of progress, I expect I'll soon be forced to revert to v8 and hope that it's just something about v9 that is causing it. Support assures me there haven't been any changes that should be having a performance effect, but then again our B&R server/proxy combo was working just fine before v9, so I don't know if I can trust them on that.
If anyone with the power to do so could escalate this ticket, please do. You may notice this post is late at night on a saturday. I'd rather not have many future weekend hours blown dealing with this.