For us to help effectively you should provide the encode command you are using at least. And even better would be a sample video clip where you are seeing the problem as well. Ffmpeg can be pretty complex and there are all sorts of options and factors.
Also did you verify the playing delays happen on other hardware as well? For example with some older nvidia cards they are unable to use all hardware decoding technologies for certain video resolutions. Namely vdpau feature set B I believe (without looking it up).
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