Is there also a difference when you dump it two times in a row without powering it on ?
Yes, there're differences between two nand dumps without powering on the xbox
Hm, thats really strange.. Seems there is any mistake (maybe you did) which we can't see yet..
Check all your wires again. Try each wire with a multimeter. Does every cable get contact ? Each cable in the right order ? recheck the diagramm. Maybe (I don't know exactly) you only get the correct flashconfig cause of the well placed diode on the boardside? Maybe there is an error in your wiring which you don't expect cause of the right flashconfig? You could ask tmbinc if he can answer this...
What sectors exactly differ?
Everytime the sectors are differents... but everytime are in a particular area where there are a lot of FF
Seems there are only dummy values. I don't expect it will fail if the differences are ONLY in this kind of areas with a lot FF FF.. (You maybe can hex edit this to FF as I expect there have to be a FF instead of BF ?) My first (broken) dump had 16 big differences which reach over multiple lines where I only got 00 00 00 .. instead of correct bytes (like dump2 or 3). So if you not got such differences, this won't be a problem I guess..
How many bad pages?
2 Pages at the same address everytime (Bad block at 0x576600 and Bad block at 0x576810)
Somewhere in this thread I read that the lower blocks don't matter.. but please read on you're own cause I may be wrong!
My 16 differences where between the 0x0AA 0x0BB area...
Is the empty pages count the same in each dump ?
Yes, everytime 1488 empty pages
Okay, I got 1427 on all dumps. Around 1400-1500 must be normal cause nearly everyone has this amount..
Is the dump readable in the flashtool (can be opened without errors) ?
Yes, I can open
all the dump in flashtool without any errors. Without the Cpu key and 1BL, currently, I can see only the CB / CD / CE / Patch 0 / Patch 1 and on the right side of the utility a list of the files like aac.xexp2 / bootmain.xex / createprofile.xexp2 and so on
Sounds okay for me.. Maybe you could find out which file is stored in your difference-area and check if this is really needed or important?
With much luck it's maybe one of the xboxlive files which you won't need in the future ? I don't know

Tried different new/old computers/laptops ?
Yes, I have tried with 6 or 7 computers / laptops (old and new)
When I tried first, I got a connectionerror on 3 computers.. So even if you get the connection maybe some other thing (mentioned above) went wrong whereas every computer will fail! (differences)
Cause your flashconfig is correct I guess the wires are all correct.
This's a good point. At least I have done the wires in the right way
But don't have to be! See above.. Maybe it seems correct but it isn't
Something other: Maybe it will help you in any case?
In my company every of my teammembers using the save java version to compile some modules etc. So we can be sure that SVN only shows that differences we want to see (expect). If I'll use an older or newer version of java the complete structure of the file is different. Everthing is rearranged then. SVN will then post every changed line which will print the complete file cause everything is compeltely different even if the file is still working.. (I'm talking about plaintextfiles which you can i.e. generate from oracle form binaries, so don't wonder which files I mean).
maybe it's something like this for you? The dump gets rearranged everytime but contains all the same data as every other dump.. only in a different order ?!
Hope you get lucky soon.. like I did after some investigation