I'm definitely feeling you with the frustration with the PC. Though I think the problems I had with mine was that I had to have a dozen different programs running in the background for my cabinet to have its bells and whistles. I had a background program for my Ultrastick 360's, another for the RGB LEDs, then Joy2Key for certain functions, etc. By the way, the programs themselves are fine. But it does introduce additional failure points due to user - read: my - error such as incorrect configurations or missing items. These don't always make themselves evident right away - such as if I decided to play a particular game for the first time and never noticed there was something funky in the game's .ini or controls.dat entry.
Parroting what Paige said, the simpler it is - both the OS and the Frontend - the more stable it is.
I'm looking forward to when I can go straight JAMMA with my future arcade projects. I was going to recently but couldn't justify the price of boards and I hate the "limited selection" of those programmable ones I've seen. (And I'm not a fan of those xx-in-1 boards at all.) There was a thread about a member working on a fully programmable JAMMA board that's supposedly relatively inexpensive that I really hope comes to fruition (too lazy to search for it right now.)
Another thing is that the cool things you can do with a PC-based cabinet (game based LED buttons, auto-switching 4/8 ways restrictors, automatic rotating monitors, and so much more) keeps me from going full-on JAMMA. That's why I'm saving it for when I can have the time to build dedicated machines (like all verticals, all Neo-Geo, a specific game, etc.) and just have to put up with the PC quirks for now.