Do you have a plugin or config that might be changing a physics variable? There are quite a few of them, including sv_turbophysics. It might be worth taking a look at what some of their values are after the problems start, and comparing it to the fresh server.
Here are some of of the physics variables that might change.
Code:
npc_vphysics : 0 : , "sv" :
phys_impactforcescale : 1 : , "sv" :
phys_penetration_error_time : 10 : , "sv" : Controls the duration of vphysics penetration error boxes.
phys_pushscale : 1 : , "sv", "rep" :
phys_speeds : 0 : , "sv" :
phys_stressbodyweights : 5 : , "sv" :
phys_timescale : 1 : , "sv" : Scale time for physics
phys_upimpactforcescale : 0 : , "sv" :
physicsshadowupdate_render : 0 : , "sv" :
sv_bounce : 0 : , "sv", "nf", "rep" : Bounce multiplier for when physically simulated objects collide with other objects.
sv_pushaway_clientside : 0 : , "sv", "rep" : Clientside physics push away (0=off, 1=only localplayer, 1=all players)
sv_pushaway_force : 30000 : , "sv", "rep" : How hard physics objects are pushed away from the players on the server.
sv_pushaway_max_force : 1000 : , "sv", "rep" : Maximum amount of force applied to physics objects by players.
sv_pushaway_min_player_speed : 75 : , "sv", "rep" : If a player is moving slower than this, don't push away physics objects (enables ducking behind things).
sv_turbophysics : 0 : , "sv", "rep" : Turns on turbo physics
vprof_scope_entity_gamephys : 0 : , "sv" :