I'm using minerd miners (no default stratum support) connected to a central stratum proxy. That stratum proxy connects to a headless linux VPS forwarding all traffic to whatever pool I choose. All I did was change the IP on the VPS to point to Middlecoin instead of Wafflepool and all of my rejects went away. So something else is going on, because my miner configurations haven't changed at all since I started mining LTC a year ago. I guess I was just having connection issues to just Wafflepool.
Absolutely not trying to call question to this, if MC is performing better for you, thats nothing I can argue with, and you should do due diligence to make sure! That said, minerd (cpuminer/pooler) has full support for stratum, and running it through a proxy will only negatively affect it. Please also make sure you're connected to the closest endpoint (closest meaning ping-wise, not necessarily geographical location).
I now realize that the cpuminer does support stratum and I was using it and not realizing it. I will verify the latency to the various servers to make sure I didn't miss something. I did wipe my VPS before reconfiguring for MC, so maybe I made a mistake earlier and couldn't find it. I hope to get this sorted out and mining back at Waffle soon. Thanks!