Also an ultra/axe2 guy. Only about a week in and I am loving this thing. Here are some axe2-headed thoughts...
I dont use the axe2 to it's full extent and the only thing I miss is my violin patch(wonder if I could profile a synth patch?). Synth blocks can be useful, but I only used it as color on a floyd tune or two. The kpa/midimate was a blast last night. I can't remember the last time I was this happy with my tone. Cut like a chainsaw through the mix-when I wanted it to. Sunk back into it when I wanted to. Just perfect. I try to keep 2 banks of 5 patches from clean to mean so I can NOT mess with the head itself for the most part. I had to turn down some bass in a patch or two but that is so simple and fast with the retro interface. After the first ten minutes or so, I pretty much stuck on my first 5, which was a Nuno clean MP1, a bogner-maybe PT bogner blue or something, and a slash jcm I think. I really was just looking at whatever names I had stuck in the midimate. A mesa orange patch I got recently and a JSX ch3 or something round out the five. I have a cool Tills engl on the second bank but I didnt get to that. Didnt need to! Over 900 profiles, and I pretty much used the main 3 last night.
I haven't had any issues like the ones you mention. I have the latest non-beta on one, and the latest 1.07 beta on the other(yeah I got two of them). Neither has an issue so far. My only complaint is that the backup doesnt completely clone one system to the other. That would be perfect. I lock my effects(on the axe2 I make one catch-all patch and change the amp/cab and sometimes drive pedals) The restore doesnt keep the ones I locked. Easy fix. Make one preset with all the effects I want and just relock those. Hope to do that this weekend. Got some wah specs off the forum and it works great.
I dont use any of the default profiles. Many sound like they are in another room, or stuff in a closet. When I find one that hits hard like a real amp right outta the gate-that is a winner. I'm sure you can tweak to get more of them that way-but time isnt something I have a ton of. I've also found profiles I really like that I would never have even wanted to based on the amp choice. The glamorous high end amps that i want to like, so-so. Some little combo amp or mp1-wow. So ignore the name, trust your ears. Also, mess with cabs. If you don't have the cabs that Tills made, get them-I like the 1960 -6 a lot. Sometimes even good presets matched with a kickin cab get even better. I always struggled with IRs on the axe2.
May I ask where you got FW 1.07? It's not on the support site?