So, are both programs capable of defragmenting a RAID 1 system using Vista 64 (and Intel Drive Matrix)?
Yes, no problem whatsoever. MyDefrag does not know anything about the underlying hardware, it leaves that up to Windows. It can therefore defragment and optimize anything and everything that behaves like a disk.
For more information see your JkDefrag logfile. Some system files cannot be defragmented, the JkDefrag homepage lists several cases and gives tips what you can do about them.