Man, this must be the 4th or 5th post I have answered on this in the last week (first one here though).
Are you converting something compressed with XviD?
My theory is that the XviD decoder is serving up YV12 video (all MPEG4 (DVD for that matter to) is YV12) and Nero for some weird reason is converting to RGB.
YV12 to RGB conversion causes the video to filp which Nero should realise and rectify. I would suggest that everyone who wants to use Nero and suffers from this effect should contact Ahead and complain untill they fix it although I agree with gerritman, I owuldn't use Nero to encode, infact seeing as we are talking about SVCD's here, I wouldn't even use it to burn.
If you do want to use Nero then you could use AVISynth to either flip the video or perform the colourspace conversion. Nero however I do not think will accept AVISynth scripts as input so you would need to use ffvfw's makeAVIS (also included with AVISynth now) to create an AVI.