If Jagex could detect 3rd party clients then people would just be banned upon login whenever using a bot.
I don't see how you came to this conclusion, you botted, you got some manual bot busting bans, you got some normal bans, and now you're perm banned, it all looks standard to me.
It's quite common to get banned while logged in too, there are some videos of it on youtube, you get a connection lost, force logged out, and banned, it's all normal.
Also in the last week or so Jagex has been cracking down hard on banning macroers for any/every bot.
I'd be more careful when making such broad claims/thread titles as to not scare the community.