As far as I know, Windows is the only operating system which has a “Time of Last Access” flag for folders and files,
I would not be surprised that there is a similar flag for removable volumes such as USB Flash Drives. Because Windows does not understand the BFS partition, it may have issues with it and leave a flag which then interferes with the subsequent boot process.
As a matter habit, I never leaves any of my Haiku USB Flash Drives attached to the system when going into Windows. This comes from having experienced some challenges booting Haiku after leaving them attached while in Windows in my early days exploring Haiku.