I finally have it working.
The problem wasn't the desktops bios not correctly recognizing the ND6500, because it did recognize the ND6500 correctly. I flashed the ND6500 first with only the maincode (the .bin file) using NecWinFlash, but that wasn't enough to use it in the laptop (the ND6500 still was master).
Later I wasn't able to flash anything into the ND6500 (although in the desktop it was recognized by the bios). I couldn't flash any 2.xx firmware, couldn't flash 6500BOOT/6500MAIN (tried with the batchfiles as wel as manually). NecFlash didn't recognize the ND6500 at all (necflash -scan).
Finally, today I was able to flash again. Flashed 6500BOOT/MAIN manually and now the drive is configured as reverse-ATA and recognized as slave. Put it in the Toshiba laptop and it's working.
The problem of not being able to flash anymore seemed to be a problem with the IDE cable. I have about 10 flat-cables which are suitable for connecting devices which are in cable-select mode and the first time I picked a good one. Today I picked a good one either, but when I wasn't able to flash, I probably picked one out of the box which had a bad connector or one (or more) broken cables, which resulted in those problems. Have tested all cables today and found the one with problems and it's out of the box now.
Just one strange thing... My Toshiba Satellite Pro 2100 doesn't give any IDE Error anymore, so the bios detects the ND6500. In Windows XP the drive is recognized and working (in DMA mode), so everything is oke. But when I boot with a dos-bootfloppy and start NecFlash with the scan option (v1.03a) it still doesn't find any vallid devices, allthough it should work with the ND6500 (and recognize it). Can anybody test this, if you have the same experiences with a ND6500 flashed with 6500BOOT/6500MAIN, all working well in the laptop and windows? Just boot with a dosflop and try NecFlash -scan (v1.03) and see if it recognizes the ND6500 or not.