I'm not sure whether there's a work around for this but it's something After Effects hasn't always done. At somepoint over the last year or two the Project window has taken to 'jumping' position, vertically, once the name of a sequence, layer or general asset has been re-named. Or when a new folder or sequence has been created. When working with a large project, with a lot of assets, this can cause a lot of frustration and slow the process down considerably as I try and re-find the area of the folder structure I was working in.
Not sure whether it's just my system, or whether there's a solution, but I would love it if it justr stayed where it was.