I recently played around with the reasons.yml and discovered that after removing one or more earlier defined reasons from the file and using /bmreload those are being re-added to the reasons.yml file.

Using 5.7.2, I know not the most current version. However there has probably nothing be changed in the code for the reasons stuff since then.

So running /bmreload is physically causing old removed reasons from the file to be re-inserted into the file?

Yes, Sir.

This is affecting all config files, looks like perhaps an underlying bug either within my BukkitPluginUtil dependency or within Bukkit's YAML library itself.

In a similar manner, you can only add players to the exemptions.yml while the server is not running. Adding/removing them and reloading will just recover the state before you added them in the first place.