I am not sure how to explain it, but i am having this problem just recentely in the last couple of 2-3 months.
I watch anime and with Fan-subs, the subtitles are merged in to it. However sometimes when a character says something, the subtitles of what he/she is saying is not being displayed. When you keep watching then after some seconds, the subtitles are being displayed again. When i stop the episode then repeat that part that the subtitles have been skipped the subtitles then sometime show correctly but then a bit later the same happens with another part.
Any idea what needs to be changed. BTW, i have only changed couple of settings
Settings changed:
General --> Video: Output driver = xv
General --> Video:Direct rendering = yes
General --> preffered audo and subtitles: Audio: jpn, eng
General --> preffered audo and subtitles: subtitles: eng, nld
Preformence --> Preformence: Hardware decoding: vdpau
Interface --> Interface: GUI: Basic GUI
OS: Linux Ubuntu Desktop 16.04 64bit
GPU: Nvidia GeForce GTX 860M
Driver: Nvidia drivers: 361.45.11
Gnome-session-fallback