So working with some sounds yesterday I noticed this problem is persisting. But thankfully this is the fix, turning off Auto Levelling prevents this from happening. Presumably as we were saying, audio gets imported as an Apple Loop or maybe Logic applies Apple Loop behaviour therefore it will auto level the Region gain.
This was happening with some audio loops and not others, so no idea what was causing the problem. A lot of my sample loops caused this issue, but I was simply exporting from Logic 2/4 bar loops at 24bit/44.1khz, which is fairly standard.
Unfortunately the issues with auto flex persist without any fix. The most frustrating thing with this is often Logic incorrectly analyses the tempo of imported regions. For example, my project tempo is 125bpm and the audio/region I drag into the tracks area is the same tempo, and then you have to manually turn off Flex and Follow or manually adjust the region.