I'm losing 50-52% packets on two internal looking IP's (10.124.**.***) before hitting EE's servers where I'm losing 3-4% before losing 6% at LINX...
The 50%
could be completely normal. Your packets are likely to have the option of taking different routes though some parts of the providers network. If there are two such routes through and on one of the routes the a router is set to not respond to pings, then you'd see roughly 50% loss from that section of the route.
PingPlotter is a great tool, but the way it works can lead to people focussing on the wrong things. For those that haven't used it, it basically combines ping and traceroute, in that it pings all the hops on the route and gives you nice graphical output.
The important thing is how many packets make it to the end, there is often less to be learned from ping packets not returned from routers in the middle.
It is hard to compare the packet loss along the route, as some of it might be "real" packet loss, with your packets not reaching the end host you are pinging and some of it from the intermediate hops might just be those hops deciding they don't have time to respond to pings aimed at them. It is perfectly normal for routers to drop some or all ping packets aimed at them (as opposed to the ones aimed at a host they are routing packets towards).
However 6% of packet loss end-to-end isn't a great indication of a well working unloaded Internet connection.