I've done everything I was asked in Yantar by the scientist and have the documents "X16". Now I'm getting back to the barman, and something strange is happening - after I gave him the documents, reputation of my character suddenly changed from "excellent" to "terrible". I have no idea, what may be the cause - I've achieved the "excellent' reputation quite quickly, and after that it never changed (I was helping various sides during rides of bandits/mutants, never refuse to give medkit someone in need, well, I'm good christian Stalker :)). And now, suddenly my reputation is ruined by this one thing.

Can I in some way avoid this issue? And by the way - what are the consequences of good or bad reputation?

Fixed in the Zone Reclamation Project: http://www.metacognix.com/stlkrsoc/

Ok, I've found an answer on another forum - it's only the "description" changed, the same reputation is still on the same degree, and its description can be changed, when it's on maximum level (but only temporary, I've done another sub-quest, and even description get back to normal).