One of the potential causes of your problems is the browser you are using. I use Firefox and there are several sites that simply "don't work at all" or only partially work. Directv and Pay.gov are two of the 'Firefox problem sites' I've identified thus far. I sometimes wonder if Amtrak.com has similar problems as I frequently get 'overtyped' portions on my screen when the top portion of a line of text is fine, but the bottom portion is overlaid with the top of the next line of text, etc. It's also possible that my screen resolution (1920 x 1080) is causing that problem.
So, if you're using Firefox, or perhaps Chrome, see if your problems go away using Internet Explorer (or whatever that new thing on Win 10 is...I'm a Win 7 user).
On other idea regarding booking with points problem...make sure you're booking as an adult, not senior or other discount fare.
And if all else fails, give 'em a call to make a reservation.