I understood that you were from Australia and going to Japan...even pointed out that my examples/tests were done here in the states. But the key aspects of routing are universal and apply regardless of what region you are coming from--and one of those key elements is that ALL traffic is shaped. Note I said "shaped" and not "throttled". Your ISP may not be throttling P2P and such...but your traffic is indeed getting shaped. It happens by design within the networking model...your OS and the protocol stack even has mechanics that contribute, much less all the ISP's own policies and even the default configurations of our routers.
Throttling is often mistaken as the shaping mechanism at play, but in fact it is only one mechanic. Packet prioritization is another...which is basically why we run tracerts. As a standard rule, ICMP is flagged as a low priority--so low in fact that some routers will start moving them down the queue as low as 60% utilization. It's not uncommon for some routers to be configured to flat out ignore it. What we look for in a tracert is for highly erratic response times along the route, which is a pretty clear indicator of elevated congestion. When you see way too much jitter at a hop, it's pretty much a given that hop is about to or already has crossed that 70-80% utilization line and is in danger of approaching congestive failure if proper actions are not taken. If it gets too bad, the very protocol in play may start clamping down on the transfer windows (that happens client side, because TCP/IP error correction is detecting pending congestive failure). These are just some other things that get lumped under the shaping category---it is simply tactics at play to help prevent congestion build up within our network sessions. Without these flow control measures, the internet would be a complete nightmare compared to how it is now. Things HAVE to be assigned a priority, or nodes will get flooded with trash and the critical data simply won't get through properly. And as we become more reliant on the internet for voice and video, it is getting awfully crowded in there...which means we are feeling the impact of packet queuing more and more as time goes by and markets continually get oversold and poorly maintained.
I was under the impression that those traces were from your "bare" ISP connection and not through a VPN service. Didn't do a dig on any of the hops, was just going by the extensions to place you in Aussie territory. If that in fact is through a VPN, then there may be a large part of your problem--as it appears you are not taking full advantage of the VPN's ability to encrypt you as you cross the ocean, so you aren't avoiding some of the issues that may be present on an unencrypted line (encrypted packets usually default to elevated priority, as it is usually sensitive/critical data like financials and such). So, if that is via a VPN, you need to pick a tunnel to a different location. Most all services will have multiple locations to choose from. Some may be limited to local region, but when dealing with a worldwide group you have them all over the place. Cyberghost has something like 1400 worldwide. Even the Canadian upstart, TunnelBear, that I have kept an active account with for some business I do online has a tunnel to Japan amongst other countries. As stated earlier, you may want to shop around if you don't like how your service holds up under scrutiny. That listing service I provided earlier has an option to filter by country if you want to see ratings from your fellow Australians.
If those traces are in fact your "bare naked" line, then your ISP is the one assigning you to that path that is having issues and there SHOULD be something they can do about that. As I stated earlier, they could/should have alternate routing partners they can use. Telstra is NOT the only service linking Oceania to the rest of the world. Last I recall, there were at least 3 major ISP's running through the Southern Cross, and a handful of others fanning out to the west towards Asia. They should have options, just getting them to change the pathing typically requires that you deal with at least Tier3 support though, so if you haven't been dealing with them (sometimes referred to as simply Engineers or maybe Admins), you may need to push for an escalation.
Edit:
Just did a quick dig on your gateway. Came up as Dodo, which is part of some larger groups (iprimus, Commander, a couple others). They have a handful of agreements with other ISP's they may be able to use to get you out of there. Didn't pull up the network maps for them, but considering they have at least 3 players in the region like everyone else in the states, they SHOULD have options other than just Telstra.
AS1221 Telstra Pty Ltd
AS7474 SingTel Optus Pty Ltd
AS9443 Primus Telecommunications
AS9482 Platform Networks Pty Ltd
AS1221 Telstra Pty Ltd
AS9482 Platform Networks Pty Ltd
(sources: http://bgp.he.net/AS38285 )
Edit 2:
OK.. just for the h3ll of it I went to the Telecom Ramblings list just to see if there were any on the list that your ISP peers directly with that has a direct path to Japan so they don't have to slingshot TATA (AS6453 in the graphics) or something...and sure enough Sing Tel shows a fairly straight-forward path to Japan:
http://business.singtel.com/coverage/googlemaps/
http://business.singtel.com/coverage/flash/
(one is a google map app, the other flash. You can select starting/ending points and it will highlight the route for you)
So, there may in fact be something different your ISP can at least TRY to help resolve issues for you. The question is will they put forth the effort.....





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