It seems the rumour of development problems with S.T.A.L.K.E.R. were not accurate. GSC Game World have clarified with the following statement.

1. The project is on the stage of beta approval and is being actively developed in close cooperation with the publisher.
2. The team has undergone certain reductions, particularly in the art section, due to all the graphics-related works being almost complete (out of 40 people 5 were dismissed). None of the leads, programmers and moreover, testers may not be reduced at any time.
3. Regarding the technology leak, none of the designers gone has the rights to the game's engine (all the S.T.A.L.K.E.R. technologies, including the X-Ray engine and S.T.A.L.K.E.R.-2 engine belong to the company). Even if the current or next-generation engine would appear on the net, their legal use is impossible. GSC does not intend to sell its technologies in the nearest time, so as does not intend to postpone the release of S.T.A.L.K.E.R.: Shadow of Chernobyl due to rumours of that kind.

Stalker-game.com