This is a known bug. To overcome it, first install the update 1.2 (if you haven't already) which is available for download at ftp://ftp.lucasarts.com/patches/pc/J3DUpdate1.2.exe
- you'll get an EXE file which you simply double-click, it installs itself.
Next, download the shambala-seal savegame file from my ftp server at ftp://ftp.soulianis.com/archive/indy/
- preferrable the .zip variant because it saves download time, although you need WinZip or pkunzip to decode it.
This should solve your problem.