I keep my vault in Box and I have this same issue (I’m on MacOS). Every reboot it reindexes. It might be an issue with the vault not being available (mounted) when Obsidian starts. When you say
it doesn’t seem to matter which drive I put the main vault on
did you try putting it on the internal/boot/same drive as Obsidian? I haven’t bothered to give that a try because the indexing issue is not annoying enough to warrant moving out of Box.