I have a boxed copy and the manual is still the a jewel-case insert. I don’t think there is an oversized manual for this game.
As for bugs – other than the saving bug (which is fixed by the patch), I didn’t run into any technical problems at all. I played on XP and enjoyed this game quite a bit. I’m not sure that setting to 256 colors and 640×480 resolution in compatibility mode will work for this game. You might have to do it manually (which is true of quite a few Sierra games) by going to the Settings tab in Display Properties and clicking Advanced / Adapter tab / List All Modes.