I'm having issues with the puzzles too - in fact I didn't realize they were the puzzles until now!
I feel like I"m behind everyone else though, as I keep mine paused during the day at work because I never know when I'll be able to check on my little people and I didn't want people dying or anything.
As far as the puzzles go I'm only on level 2 for harvesting and am working towards getting level 2 for science next. I don't know HOW in the world I'm going to get level 3!! Those tech points seem insane. I'm running at normal speed on low difficulty though and others have said this level seems to be the lowest on getting tech points. I'm hoping once I get level 2 science that I'll be able to do SOMETHING to the boulder, etc as it usually says "additional research needed" when my little villagers try to do something.
Am I correct in thinking that some higher levels will get me somewhere? I don't want a "spoiler" - I like the surprises I've been getting by avoiding the spoilers, but I'd like to know I"m on the right track at least