Inside the Divide Between the Kardashians and the Jenners

"Some of the kids are more comfortable [with the transition] than others," a source tells PEOPLE

Photo: Chelsea Lauren/WireImage

Bruce Jenner might have said it best on the season 10 premiere of Keeping Up with the Kardashians when he said that he felt “so separated” from the Kardashian family following his split from Kris Jenner. “Kardashians over here and the Jenners over here,” he told stepdaughter Kourtney Kardashian. “Little me in the middle.”

Their exchange reflected what was going on behind the scenes: Bruce, 65, was undergoing a gender transition and the Kardashian side of the family, though supportive, was having a difficult time dealing with the bombshell.

“The whole transition was much harder for the Kardashian kids and Kylie and Kendall,” a source close to the expansive Kardashian-Jenner clan tells PEOPLE. “It was hard to grasp. And there was a lot of lying to the kids over the years on Bruce’s part, even as close as they were. It’s going to take some time for the kids to get used to it all.”

Following the broadcast of his 20/20 interview with Diane Sawyer in which he revealed his intent to transition, every one of his family membersincluding Kris – extended their support to Bruce, be it by Tweet, Instagram or Today show interview.

However, one member of the family appeared to resent the sudden influx of support. “Having a hard time not putting a few people on blast who were not supporters beforehand, but want to act like they were all along,” Bruce’s son Burt Jenner, 36, wrote in a now deleted Tweet that appeared to be directed squarely at the Kardashians.

Bruce Drifted Away from His Eldest Children While ‘Struggling’ with His Gender Identity

Bruce had drifted apart from his four eldest children – Cassandra, 34, Brandon, 33 and Brody, 31, along with Burt – during his marriage to Kris, but they’ve gotten closer in recent years. “The big, formative years for them, I was really struggling with those issues [of gender identity],” said Bruce in bonus footage from his 20/20 interview, as seen on Monday’s Good Morning America. “I didn’t do a good job. And I apologized for that.”

While it was all water under the bridge for Brandon, he hinted at past tension in his siblings’ relationship with their father when he said in the footage, “In seeing him come out to me and explain his true self, I was more proud right then to carry the last name Jenner, to be a part of the family, than at any time before.”

As Bruce got closer to his children with Chrystie Scott and Linda Thompson, his relationship with his Kardashian stepdaughters, who “were the last ones let in on it all,” as a source previously told PEOPLE, has changed.

That said, “it’s been a process for everyone. Some of the kids are more comfortable than others,” the close family source tells PEOPLE. “But in the end he is, and will continue to be, a better father, better person and human being.”

Once again, the KUWTK premiere foreshadowed the family drama that would come to light one month later when Kim Kardashian West said: “We just have to get used to our new normal and figure out what our new family dynamic is and we’ll all figure it out and will all be fine. It’s just going to take a minute to adjust.”

Editor’s note: Per Bruce Jenner’s request, PEOPLE will continue to use male pronouns until otherwise instructed.

For much more of Bruce Jenner’s new life, including what his ex-wives really knew, pick up the latest issue of PEOPLE, on newsstands Friday

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