In the german section the users were explictly advised to start anew after 1.6.x to avoid severe problems.
Iit might be that this warning wasn't related to the Steam-users as Steam was released some days later and the 1.6.x update came only hours after the introduction in Steam (instead of days for the DVD).
Even if your problem isn't related to the differences between Steam and DVD: it is most strongly advised to start anew _after_ the update to 1.6.x as the release (1.5.x) had some _very_ severe problems which sadly persist in the savegames, too!