Hardware transcoding quality

I have a question concerning the quality of hardware transcoding. I have an intel i5 4690 with a hd4600 gpu.
I noticed a very visible degration in quality of the transcoding sessions after hw transcoding came available to the public version of the media server.
The beta versions of the server had much better quality.

Is this a known issue?

Guess i am the only one who noticed this?

I am aware that codecs,bitrates etc all have influence on the quality,thats why i compared the same video file in the beta version and the newest Plex version.