I noticed that all the problems here are always the same, setup, drivers, lags under certain parameters.
The 'hacked' version is just a installer+tweaks, some details and source code is available in http://servicios.ried.cl/arduino/ (excepting the library manager source, because I am still experimenting with this, will be nice to add a complete repository so you type a library or chip code and you instantly get the library 
haha but still it is too much work)
Also I tested the setup in an XP vm and Win7 x64 and x32, so the main idea is to reflect a "perfect" installation in your system, so if you get issues, at least those issues will not be the common ones.