I searched in many place but I don't find an answer to my question. Same question has already posted here : https://serverfault.com/questions/534507/vagrant-nfs-share-doesnt-show-updated-file-if-size-doesnt-change
But the solution is only for Sublime Text. I use Jetbrain PhpStorm 8.
The problem is exactly the same, my NFS doesn't detect my file change if the file size doesn't change too.
Already two weeks with this problem, it will make me crazy.
A bit late, but I had the same problem and I found out that underlying winnfsd.exe library that vagrant uses is bugged (as you can see here: https://bitbucket.org/jankowfsky/winnfsd/issues/7/winnfsd-doesnt-always-overwrite-files).
There is an updated library which has the bug resolved here: https://bitbucket.org/yannschepens/winnfsd-new/downloads
You need to download updated library and replace existing library, which is located on your disk in the installation directory of vagrant-winnfsd plugin - for me it is
C:\HashiCorp\Vagrant\gems\gems\vagrant-winnfsd-1.0.11\bin\winnfsd.exe
So, just take downloaded winnfsd.exe and replace existing one. Fire up vagrant and problem should be solved.