Remove all superfluous plugins. Try looking at the CAL server config too. sys_ticrate - raise this as high as you can while maintaining a stable server FPS.
This worked well to fix bullet/bite registration for my server (linux): <!--c1--><div class='codetop'>CODE</div><div class='codemain'><!--ec1-->./hlds_run -game ns +sys_ticrate 400 +fps_max 100 +ip x.x.x.x +maxplayers 27 +map co_faceoff<!--c2--></div><!--ec2-->
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sys_ticrate - raise this as high as you can while maintaining a stable server FPS.
<!--c1--><div class='codetop'>CODE</div><div class='codemain'><!--ec1-->./hlds_run -game ns +sys_ticrate 400 +fps_max 100 +ip x.x.x.x +maxplayers 27 +map co_faceoff<!--c2--></div><!--ec2-->