I've been having the same problem, I've made sure I've selected the right connector, here is my current ship https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2327193423

I'm wondering if its a lack of thrusters, the whole craft ways just over 300 tons, and there are adequate thrusters in all directions, besides facing upwards, where it's lacking around 100 tons of force.

I'm also using a mod that adds mass to hydrogen in tanks, perhaps this is an issue with a constantly changing weight? I'm not sure if you have the mod, but it's information that could be relevant.

I'm also using connectors from a mod, could that potentially be contributing to this?

EDIT: The problem was being caused by the custom connectors, it is fixed now