Well, I don't think you've jumped into a leaky boat. It's understandable that you're finding OSX confusing after years of Windows. It takes some getting used to, but I find OSX much much more stable than Windows and I use both daily.
Every now and then, permissions will become corrupt/false and simply repairing them using the aforementioned method
always solves the problems. The most likely reason that it happened is because you may have installed a third party program that messes with your system. As far as I know, it's only the installers that require your password that have the ability to alter permissions unlike the (very hazy) Windows equivalent, the DLL (I use the term very loosely, they're quite different), which requires no user password meaning any app can do what it likes with DLLs, plus it has no utility to fix idiosyncrasies.
In short, a similar error in Windows would have been
much harder to fix.
The good news is that once you have installed all your apps, you shouldn't be getting this problem as frequently. However, I personally have never had this problem so maybe it's a specific problem with one of the apps you
have installed. What have you been using/installing recently? There could be an incompatible pieces of software on your Mac which is causing this.
Absolute summary (I promise): I have no idea what specifically caused the problem.