I have some problem with interoperability with certain executables that seems to behave somewhat randomly. Along the way, I stumble upon Process Monitor. From it's descriptions on the site :
"Process Monitor is an advanced monitoring tool for Windows that shows real-time file system, Registry and process/thread activity".It proves very useful in my case. It shows that somehow there is registry activity that explain the cause of the previously random behavior.
It's another useful addition to the toolbox along with other utilities from Sysinternals that I have been using so far, most notably DebugView and ProcessExplorer.