Acronis did its job, it copied bit for bit what it saw....a boot drive which always has the 100 MB for windows to use for repair. So you removed the old drive and saw that you had a 100MB partition, this is normal. When you CLONED the drive, you made it the new system drive to replace the drive that is failing.
Except its not my boot drive, its another data drive. I have 2 drives in the system, a 128GB SSD formatted as GPT it has 3 partitions on it, (128MB hidden (BitLocker or GPT Partition info?) 100MB EFI Partition and then 117GB for OS), the second drive is a 1TB WDC formatted as MBR with 2 partitions (128MB hidden, and the rest is Data).
What is throwing me off is that I can format the drive in Windows as GPT and it wont create the 100MB EFI partition, but when ever I use any sort of cloning software, it creates the 100MB EFI, even when it is told it will be a DATA only drive.