I had the same problem when trying to replace rear gear cable. I had already done the brake cable, which went through the frame very easily. After much head scratching I took the forks off and found that the internal routing guide tube was not fixed in the frame at the headset – simple to fix, albeit fiddly.

I had the same problem. Issues with set up on to different bikes from different suppliers when bought (internet) – solved by:

Adjusting the B tension (the gap tool is very useful, and Eagle does seem sensitive to this adjustment

Getting the correct chain length – the stock length on my bike was too long

Confirm the cassette torqued correctly, and does not have any play.

I was told by a bike mechanic that this issue is not uncommon and is apparent with the bike in the stand (he said he had queried this with SRAM). Under more tension when pedalling, the chain will engage and tends to settle down as the cogs and chain wear, however, it is more like a set up issue.