What version of the game are you playing? The number is displayed in the bottom right corner of the main menu; 1.47 or 1.49 are the latest version (the 1.49 patch removed the copy protection, but made no changes to the game itself compared to the 1.47 version). Note that if you install the 1.49 patch over the 1.47 version of the game, the displayed game version in the main menu may not change (that is just a cosmetic issue, though; if you can start the game without the Play CD/DVD, it installed properly).
In the unpatched disk version of the game loosing the teleporter stones entering act 3 was a known problem, but with the
patch installed, an updated re-release disk version or the download version, that shouldn't happen.
Whether it was a bug, glitch or you just lost them, it is possible to get a replacement set of teleporter stones with a little bit of file swapping (in a new save, to be safe). See the
Inventory files topic, with the required files (there are two links for the teleporter stones, one for act 2 and one for act 3) and a link to the instructions.
You will loose the teleporter stones by design when you enter act 4.
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