I can't say *why* it's happenin,g but as someone who makes a ton of long threads, I know exactly what you mean.
I notice it tends to happen when I've just switched back to my official thread tab, so what I've gotten in the habit of doing is making sure I double-click on the very end of the thread. That works for me every time, although it gets to be quite cumbersome.
If it doesn't, you can also try going to the end of the post, hitting Enter, and then clicking on where you want to continue working on. It's annoying, but it always gets the job done for me.