Well so far it's been working fine, I haven't had it not work in the three times I used it since posting.
On a mission two nights ago I kept changing the .speed and going in and out of ALT-X auto pilot mode to see if I could get it to reproduce the symptoms I had a week ago. Nothing, the dang thing worked perfectly like it always had.
I can stay in ALT-X mode and the .speed commands will change speed - which is my understanding of how it is supposed to work. Now if I am NOT in that mode, the only time .speed alone has any effect is if I'm already in the default climb you end up in with auto takeoff engaged. I presume that is because you ARE in that mode, you just didn't have to type ALTT-X to get there.
If I type .speed xxx when not in that mode of autopilot, I won't see anything until I use that mode, and then it will seek the speed I typed (same flight).
So that's how it's working now, but didn't a week ago. I have no clue why it did that, use same commands, my controller didn't catch fire or anything, so I guess I chalk it up to just one of those weird things. I'd hate to think my controller is imposing it's own version of ENY with autopilot modes.
Thanks for all the good info in the replies to this thread, and thanks for checking back with me.