I've received some reports on some of the achievements not working correctly.
Thanks for reporting it, sorry about the delay in getting it fixed. I'd like to blame some problems with the original project files (which I had), but the truth is I've been swamped with the developing of Sylvio 2.
Now however, you should receive any and all achievements you are entitled to when entering the start page. Just let it sit for a couple of seconds while it goes through your save data.
Let me know if there are any issues with this (or anything else) at firstname.lastname@example.org