Working with Vagrant be like:
Oh I see you've added new features all over the project files, all good, I'll sync that to the virtual folders. Oh now you've added a line to the css, would be a shame if I stop syncing now for no apparent reason and let you go insane figuring out why the minor change won't show

use nfs synced folders?

Thank you for your kind suggestion, that was one of the first solutions I've tried. Using the NFS synced folders, it usually works like a charm, and when the issue appears a simple Vagrant reload solves the issue. I'm suspecting it's more of a issue of Vagrant running under Fedora, since the same config file works with no fail on some other distributions.