There should be no functional differences between capturing and deploying to raid-1 vs raid-0. FOS should deploy properly to both. If you think, you are able to deploy raid-1 and its OK you might want to ensure that your array is intact.
I could understand how it might deploy in a raid-1 situation and fail in a raid-0 because of the way the intel raid works, in that it presents the disks as individual regular disks (/dev/sda & /dev/sdb) AND the array disk (/dev/md126).
I wrote a tutorial on how to configure FOS to deploy to systems using the intel raid array disks here: https://forums.fogproject.org/topic/7882/capture-deploy-to-target-computers-using-intel-rapid-storage-onboard-raid
Did you use this method to deploy to the raid-1 systems?