Are you saying set to non-RAID and do chkdsk /F on both of the drives then turn RAID1 back on? I have the same problem after the machine wakes form sleep. The Intel RST goes into Verifying and Repairing for about 8 hours.
Mainboard ASUSTek GRYPHON Z87
Chipset Intel Haswell Rev. 06
Southbridge Intel Lynx-Point-LP Rev. 04
LPCIO Nuvoton NCT6791
BIOS AMI Ver. 081, date 04/19/2013
CPU Intel i7 4770
Windows 8 (6.2) 64-bit (Build 9200)
Volume1, RAID 1:
SATA Port 2 WD Caviar Green 2TB Model WDBAAY0020HNC-NRSN
SATA Port 3 WD Caviar Green 2TB Model WDBAAY0020HNC-NRSN
SATA Port 1 PNY SSD25C120GC1DH16T2-T
The Intel® Rapid Storage Technology or the RAID function should not be related to the Sleep mode or S3 State; however, I will forward the feedback to the corresponding department for future considerations.
I would recommend you updating the drivers in your system including the BIOS chipset and also, as mentioned before, setting the Disks to non-RAID and testing the system.