Ya i am also facing this strange problem.
I just started exploring sitefinity 5.0. Project manager results something(improper one), and visual studio results something(Proper one). now i simply use project manager for creating/importing projects only, not for checking out sitefinity backend/frontend.
I'm also facing issue for sitefinity thunder extension. Everyday i have to change port number of my sitefinity project in sitefinity thunder connection in order to work with thunder. i could change port number for the project loaded in visual studio. surprisingly, sitefinity thunder takes port number which sitefinity project manager manages. And i don't know how can i fix the port number for the project loaded by sitefinity project manager.