I'm wondering if the songs that aren't there are ones that only exist on your phone? I use google play's music mananger on my PC to upload all my non-google play music and then it is available on all devices and I've never had any problem with songs not showing up in playlists on any device. I can create playlists on any device and they will show up in full on all other devices, including the web version of Play Music on my PC. You can upload 20,000 files with Music Manger (they don't even count music you've gotten from google play music in that number) and it is free. So if your problem seems to be related to the question I asked in the first line then you may want to try that.