I've never used them before.  Will this improve over time as they get broken in and frayed?

Is this a typical problem others have experienced?

I usually use rubber whiskers but was just wanting to try something new.

Teap

Anytime you change anything on your string you may have to re-tune. You may have to adjust your nock height and/or your brace height.

I have never had this issue before, but agree what was said by KentuckyTJ in that you should retune when making any changes to your setup...I would not have thought that would have mad a difference though.

It has changed the tuniing as suggested.  Brace height more than likely.  God Bless

You can try moving you silencers up and down a little at a time and see if it helps.

Going from rubber whiskers to yarn silencers has most likely made the string lighter; thus a little faster and perhaps altered your tuning.  Other than that, I've never heard of any type of string silencers causing erratic flight problems.

Yeah I have had to retune for exactly the reason cited by swamp yankee above.