I believe that the .map files only effect the NPC's Line of Sight, which should not effect melee damage in any way. It only effects detrimental spells and KoS NPCs. Neither of those can work without .map files.
What is the message you get then whey try to hit you? Is it something like "Name tries to hit YOU but misses!"?
The only thing I can really think of is maybe you are missing some required SQL. You found this problem right after you installed the server for the first time before you made any special changes at all? Are you running a dual core CPU or Windows Vista on the server PC?
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