I tried the game, went to free play played a little, saved, quit, played dif game, reloaded settlers, loaded game perfectly on the latest 1.1.2 if this helps.
When I play another game and then play Settlers again. I know there is a thread about the same problem I'm having. I believe the problem is listed as being the same one pokemon ranger had.
I'll have to test it out, and yeah, Theme park does take a long time to save. Settlers takes a while as well. It looks like there's only one save slot for free games as well. Still an awesome game though.
Test it on 1.0. I tried it on an earlier firmware though, and it still did the same thing. Maybe you've just got a lucky cart (or I have an unlucky one).
Sadly you're going to get the same corruption error using FW 1.1.0 unless you uncompress your Settlers save before "Step 3". Of course this is just a workaround until "DS-X team" decide to include an user option to use uncompressed saves or fix their crappy "EEPROM engine" once and for all.
I would be interested in the results for the "experiment" in my previous post from jawas or loathsome (they claim no save corruption issues for Settlers on FW 1.1.2). Using Pokemon D/P before playing again Settlers matters, because of Pokemon save size.