Well I've ordered from Logistic many times and have never had any major problems with them. I would suggest maybe calling them and seeing what they wanted. They may have just wanted to confirm a size, or inform you that they don't have the size in stock therefore it will either be backordered or cancelled. Could be anything. You can check on the site (once you've logged in) the status of your order, like if its been shipped out already, or awaiting shipping. Have a look at that, it may answer some questions for you as well.
Yes, you are correct with the yearly alloted point system. you can use these points to get items, keep in mind that this is where your DEU replacement clothing will come from, so don't waste all your points on t-shirts or shorts, when you may need some fresh dress shirts later on in the year. I believe that the Logistic site is to replace the DEU orders from clothing stores, not supplement it. Keep that in mind.
You can also purchase items for money via a credit card, but its really not worth it, since you have the points.
Hope that helps.