The manager is at a loss to explain why his side are making a habit of conceding the first goal this season, but is happy enough with an impressive start to life back in League One.
"It's all about winning football matches and we are managing to do that, even though we keep falling behind," said Clarke.
"That is no fluke. The fitness and character of my players is top class and they are also able to switch formations when things are not going for us.
"I seem to be saying the same thing after every game because they never know then they are beaten.
"I can change things tactically, but it is down to them to implement the changes and they keep on responding so positively.
"We switched off for their goal and it was a poor one to concede. But yet again the lads have shown tremendous spirit to get what they deserved in the end."
Substitute Ellis Harrison was Rovers' hero, volleying a 90th-minute winner. The Wales Under-21 striker met a left-wing cross from another replacement Cristian Montano at the far post and hammered a shot in off goalkeeper Jonathan Bond from the corner of the six-yard box.
Gillingham had taken a 62nd-minute lead when Rovers failed to defend a long throw from the right and Josh Wright popped up unmarked at the far post to fire low past Kelle Roos.
Man of the match Chris Lines grabbed an 82nd-minute equaliser, exchanging passes with Matt Taylor and breaking through the middle before coolly shooting past Bond.
Gillingham had seven players booked and manager Justin Edinburgh admitted it was a tough defeat to take.
He said: "I am hurting for my players. With the amount of effort they put in today, they didn't deserve that.
"I couldn't ask for more in terms of work-rate. We paid for being caught out of position for the goals and it is just split second lapses in concentration that are costing us
"It can become psychological when you keep giving away leads and we have to deal with the mental side of the game at the moment.
"I have to lift the players quickly ahead of another game on Tuesday, but if we keep playing like that the results we want will come.
"I thought only one team looked like winning the game when we scored and it is a tough defeat to take."