I have experienced the same frustration and it is really annoying, especially when you are charged for something without even knowing if it's in stock.
On the other hand as an IT guy in a previous life I can tell you implementing a real time inventory system is both expensive and requires a lot of time to keep accurate. You need all the hardware, software, training, maintenance, etc, etc. I don't doubt Charlie's statement for a split second that they spend a lot of time and money on their inventory system. I can easily see where the costs for such an inventory system might be too much for smaller suppliers to absorb.
Sometimes a telephone call saves any hassles. I'm lucky that I live relatively close to one of our sponsors here in Georgia - Legacy Station. If there is something specific I am looking for and don't see on their site I just call them. They have always been very helpful both in the store and over the phone to go off looking to confirm they have some thing I am looking for.
As good as they are, my aim is not about plugging Legacy but rather to make a point. Find a supplier you really like and try and stick with them if you can. I've found doing that has eliminated so many hassels regarding sales and support and helps keep playing with trains fun.
Ed