The main issue was poor planning; Larian assumed that certain OSX middleware also existed for Linux, and was included with it. That was not the case. There were a few issues with middleware along the way, in addition to the time needed to program the stuff that didn't exist.
By the time the Linux version was done it was very out of date, so needed to be updated. There was the already outdated release version of D:OS, or the current code base at the time for the EE. It wasn't feasible to update it twice, so it was delayed again for the EE, since at least that way it would be the most up to date game version, and the current engine would be ported, making it possible for future games to support Linux.