If there really isn't any visible problem with the wiring as you said, then it's definitely the switches. The chance of anything being wrong with the PCB itself is really really unlikely.
Omrons are typically used in Japanese arcades and will take a bit more pressure to register than Cherries. For instance, if you graze the side of a button with a Cherry switch installed, it will likely register while with an Omron it probably won't.
Some say Cherries last longer, but I don't see how this would be the case. If anything, a worn in Omron should feel like a Cherry.
At any rate, I prefer Omrons for the solid click and elimination of any mushiness. However, if you like to lightly slide your hands across the buttons for certain parts or don't tend to use much force, Cherries would be your best bet. If you want to order some, try
Tornado Terry's. The site looks awful, but it's legit. I don't personally know of any places to get Omrons though.