Anybody use a stereo amp with their ht? And ..

Noticed that ht sound quality is diminished when having main speaker cables routed thru the stereo amp via ht bypass setup?

I say this cause I hooked up a stereo preamp and noticed that ht sounds are diminished after signal flows thru the stereo preamp.  Anybody see this too?  Stereo did sound a lot better since it no longer was connected to the avr.  Guess you can’t get ht and hifi great sq when linking ht and hifi systems together.  
Thanks.