Seems to be 8 years after the original post and the problem resides.
The use case is a large loop processing thousands of files. From each file, some parameters, stored as binaries in specific fields that Mathematica cannot read them directly (unfortunately). So, I use a Perl program for that (exiftool). The call to exiftool succeeds for sever tens of times and then it fails, returning nothing (empty string), and this effects the rest of the program.
It happens for me with Mathematica on the MAC, Mathematica on PC Linux AND on the WEPC. The response of the EPC is the worst of all, since the response time of calling RunProcess under heavy load is the worst of all. Second worst is the MAC, because it is too fast. A modest 3 years old Linux machine is the best, but still multiple failures happens.
When I insert Pause inside the loop, just before the call to RunProcess it reduces (just reduces, not cancel) the number of failures BUT the performance of the program is reduced accordingly.
Hope WRI have a better workaround for that issue.
