VBSP is failing horribly at some point, it's not even finishing its stage of the compile process. What VVIS and VRAD then do is take is your last version of the map that did compile and present it as an "updated" map even though it isn't. That's why the physics usage is still at 112%: it's still using the old bsp.
I suggest you do what Killohurtz told you to do a couple of post above: fix leaks, to-world displacements, fix the areaportal errors, the whole lot. All of those will cause a compile to fail causing VVIS and VRAD to use the old version and just recompile the vis and lighting data.
Get rid of the compile-crashing errors first, then worry about fixing the physics errors (also stated above on how to fix those by Werewolf and Crowbar).