Might be the front derailleur rubbing slightly against the chain when pedaling that's causing the clicking. Could be a mis-adjustment, or you need to "trim" adjust the front sometimes while riding. As you shift the rear, then chain can sometimes rub the front.

BUT, you need to diagnose and explain the "clicking" better, because there are lots of possibilities.
Could be as simple as the surplus front derailleur cable hitting the crankarm in certain gears.

There are soooo many variable when comparing 1 bike to another, that it's not usually the bike itself that accounts for different "speeds".
Posture, wind shifts, tire pressures, traffic, fit, along with all the human variables from 1 day to the next... mood, sleep, food, time of day, stress ......