The Steam / Larian Vault release today is a new version.

Lar mentioned in a status update some time ago wanting to release another update for the download version after 1.005A, but finding the backup of the source code was accidentally for the disk version, rather than the download version. Consequently, they had to re-do all the changes to add widescreen and higher resolution support, etc, and added Windows 7 support. There is no list of changes yet, that I've seen, but the configuration program is a mix of the earlier download and disk versions (select resolution, software or Direct3D mode, and a couple other options).

The new version (1.006A) does not run under Win98 (not that that will be a horrible shock to many). The GOG installer requires XP or later, but the game itself (1.005A) was fine in Win98.

There has been no word yet on if or when the GOG version will be updated.