I believe there are a number of firmware updates. I recently updated my 5005B to the UK 080 and drive firmware which became available at the same time as the 098. I believe either there are two UK scart machines with different firmware or you have upgraded to the US version now at 098.
In the online manual the US version does have progressive scan - the UK scart version does not.
My setup has always defaulted to PAL and region 2 after upgrading from the original 071 firmware then 076 and now 080 (which I hacked to give 3Hr and MV free). Is yours the same or did it default to NTSC and region 1?