High fluctuaction in fps can cause that I believe, try capping your fps at 60-70. /com_maxfps X
There are some other things which may help (Note: these are just from what some server mods/admins spammed at people lagging);
512mb of ram: /com_hunkmegs 300, 1gb of ram: /com_hunkmegs 600
Allow maxiumum data flow:
/cl_maxpackets 125 (Default 30)
/rate 35000 (Default 3000)
/snaps 40 (Default 20)