I've removed the settings and restarted the miner, after 18hrs using the settings I'm at 3.5% reject. Shall be interesting if I'm around 3.5% after 18hrs with the settings removed.
For what it's worth, my Linux rig with 280Xs is currently sitting at a 3.15% reject rate - with all three settings at default.
My Windows rig with 290s is over double that, at ~8% in the same time span and from the same connection - also with all three settings at default.
On Wafflepool I saw around 0.5% on the 280X rig and ~1-2% on my Windows rig. On a regular non-switching mining pool those numbers are cut in half, nearly zero on the 280X rig and below 1% on my Windows rig. With the exact same settings that gives me 3-8% on this pool.
I'm not entirely certain why there is a difference between the two systems, but I suspect the issues may lie within the differences between both OS' TCP configuration. At least I know there's been issues with Windows and it's TCP implementation previously. There's also been several fixes* for online games previously, another genre that also requires a fast and stable internet connection. Note that this last paragraph is just a wild guess on my part - I'm merely curious and raising the question, I haven't done any leg work yet.
*
http://www.sk-gaming.com/content/15500-Smart_fix_allows_you_to_drop_your_ping_by_150*
http://www.justanswer.com/computer/3du1a-rid-200ms-delay-tcp-ip-ack-windows.html