Is my cat having trouble swallowing?

Our 7-month-old kitten started doing something odd two days ago. After lapping up water, he'll extend his neck and make repeated swallowing motions–often comes with a "clicking" sound. No gagging, regurgitating, or other symptoms as far as I can tell. He seems to swallow food (wet and dry) just fine. Appetite and energy are normal.

He recently went to the vet because of sneezing and a whistling noise... vet suspected a URI (possibly from the herpes virus?) and he just completed a course of antibiotics and is still on Viralys Lysine powder. 

Could these be related? Should I worry and take him to a vet immediately? 

Thanks so much for your help. I worry about my little guy.

It's really hard to say without seeing him "in action".  But if he's doing fine when he eats, maybe this is just something he's kind of playing at?

I know when one of my cat drinks water, he coughs, but only when he drinks.  The rest of the time he's fine.  I even had he Vet check him out and they couldn't find any reason for it.  He's just goofy