Its nothing to do with SE is it, check this trace from the feeback thread
1 1 ms 1 ms 1 ms 192.168.2.1
2 8 ms 9 ms 8 ms 10.4.127.254
3 333 ms 123 ms 53 ms 10.137.196.145
4 14 ms 9 ms 11 ms 10.255.49.94
5 874 ms 142 ms 9 ms te2-8.ccr01.opo01.atlas.cogentco.com [149.6.32.17]
6 13 ms 13 ms 16 ms te7-1.ccr01.vgo01.atlas.cogentco.com [154.54.57.138]
7 24 ms 23 ms 23 ms te4-8.ccr01.bio01.atlas.cogentco.com [154.54.37.49]
8 27 ms 27 ms 27 ms te2-2.ccr01.bod01.atlas.cogentco.com [154.54.38.82]
9 36 ms 38 ms 35 ms te0-0-0-1.mpd22.par01.atlas.cogentco.com [130.117.0.226]
10 108 ms 109 ms 109 ms te0-6-0-2.mpd22.jfk02.atlas.cogentco.com [154.54.46.105]
11 114 ms 115 ms 114 ms te0-3-0-6.mpd22.dca01.atlas.cogentco.com [154.54.41.29]
12 160 ms 154 ms 145 ms te0-2-0-3.mpd22.atl01.atlas.cogentco.com [154.54.2.101]
13 145 ms 144 ms 145 ms te0-3-0-2.mpd22.iah01.atlas.cogentco.com [154.54.2.246]
14 194 ms 176 ms 175 ms te0-0-0-3.mpd22.lax01.atlas.cogentco.com [154.54.45.6]
15 179 ms 179 ms 183 ms te9-1.ccr02.lax05.atlas.cogentco.com [154.54.44.130]
16 181 ms 181 ms 180 ms 38.104.84.42
17 289 ms 289 ms * gi11-0-0.cr1.nrt1.asianetcom.net [202.147.61.170]
18 289 ms 291 ms 290 ms gi1-0-0.gw1.nrt5.asianetcom.net [202.147.0.178]
19 295 ms 295 ms 298 ms squareco.asianetcom.net [203.192.149.210]
20 316 ms 310 ms 683 ms 61.195.56.129
21 310 ms 298 ms 307 ms 219.117.144.2
22 296 ms 296 ms 297 ms 219.117.146.149
23 306 ms 308 ms 308 ms 219.117.146.129
24 310 ms 308 ms 307 ms 219.117.146.46
25 447 ms 416 ms 317 ms 202.67.52.81
Now I know it is only one but it breaks your thorey apart you will see yes it jumps when it gets to Japan to a min of 109ms, but then ir gets to SE's ISP and it jumps 100ms, then it gets to the on to SE's network and jumps to 683ms, i'm sure there will be more traces like this which show there is something at SE's end.