1- I'm not sure how you are seeing the RAID drive properly in Linux. Almost all RAID drive currently available require special RAID software drivers to be installed under Windows. If you need these drivers under Windows and Linux does not have RAID drivers that prefectly match the WIndows RAID geometry then you will get strange results (and you seem to be getting strange results).

2- Some files that can exist on a NTFS system can not exist on a FAT32 system. Are there any files 4 gig or larger on your system? If so they cannot be moved to a FAT32 system as it simply does not support files 4 gig or larger.