I had this happen again this morning using Mode 1, where climb altitude never happened. I don't think I missed any instruction, but I can't decipher the log file to figure it out. I was cleared to initial altitude of 13,000 and that was it, no more altitude changes and my flight plan was for 36,000 which I checked in PF3. Then no hot keys worked after that for altitude changes.
This happens to me quite a lot of the time and I've found it's to do with not hitting your transition altitude. Depending on what you have your transition altitude set for the country you're operating in makes you not hit the initial climb altitude, so ATC just sits and waits until you hit the altitude. If you've set the transition altitude for say 6000 and you correctly switch over to standard pressure once you reach it, but the country you're operating in has a different transition altitude especially if it's higher, you're always below what ATC has cleared you to. If I make this mistake, I switch the pressure back and climb up the few hundred feet. As soon as I hit the altitude, I always get a response from ATC to continue my flight plan and they then clear me to the next level.
It seems to work for me every time I have this issue.
Hope it helps