You must've tried the active 3D glasses that was running low on battery. Not everyone notice the flicker on the active glasses but I guess you're one of the unfortunates. You can try passive 3D. I haven't heard of anyone having problems with passive glasses. Currently, LG and Vizio makes passives. Look at LG if considering another 3D TV.
There are flicker free 3d tvs. It is called passive 3d tvs and those with flicker are called active 3d tvs. Active 3d tvs are usually from Sony and Samsung. Passive 3d tvs on the other hand are from Vizio and LG. Earlier this year, Panasonic started producing passive 3d tvs too. To some people, flickering is not really an issue but I understand your concern because I also find it distracting. I have a 3d tv too which is also a smart tv at the same time but I got mine from LG. I like that their tvs are user friendly and the designs are elegant.
I had a chance to watch Samsung active 3D TV at my friend's place and I didn't notice any flickering at that time. But my friend told me that whenever the shutter glasses start to run out of batteries, the shutters on the lens move really slow and flickering is noticeable.