First of all, this bug has been occuring on certain game systems since KMOD 1.0, and can be fixed by warping to the next map most of the time. Also, it most probably wouldn't occur on a properly setup KMOD installation, i.e. copying a properly patched Hexen 1.1 wad in a dir and then extracting a full release KMOD version into this dir. If your Hexen.wad is 1.0, you best install the game fresh from the CD and patch this wad with the patch you can find the link to from the Hexen section here at RavenGames.
In your case, at the exit portal of Seven Portals, save your game, then pull down the console and type in
That will take you to the right shop from which you can exit directly to Shadow Wood through the normal teleport in the map.
As for the bug, I think it's an original Hexen one, you could confirm this by entering the end portal when your screen is red from a hit a split second earlier (or it might work with the green tint from the Cleric's flechettes). I think it'll be a bug in DOS Hexen as well. Anyway, I added it to the list of KMOD 2.2 bugs (which is thankfully short and consists of similarly little thingies). There'll be a patch version of KMOD 2.2 next week or so, you'll be able to apply the patch to a full 2.2 installation just as fine as to a 2.1 one. At that point, I'll replace the current 2.2 full release download file as well, though there will be no new version numbering for this (who the **** wants a 2.2.1 version? [img]images/smiles/icon_wink.gif[/img] ).