Hello thedailynathan, we have a mechanical drive with 2 NTFS partitions and we were able to accelerate the drive without losing any of the partitions. The best recommendation for this scenario is updating your Intel® Rapid Storage and BIOS versions (so the RAID option ROM will be updated too); please check with your system/motherboard manufacturer in order to get compatible updates.
In case the issue persists please provide more information about your system configuration, such as: system/motherboard model, chipset model, HDD/SSD models, partition types used (NTFS, GPT, EXT4…) or a screenshot of Windows* Disk Management.
This thread will be moved to the Intel® Chipsets Communities since its chipset related software and usually SSD (brand/model) transparent.
The motherboard is the ASRock Z68 Pro3. BIOS is fully upgraded to the most recent 2.10. The storage configuration is as follows (set in RAID mode in the BIOS):
180GB Corsair Force GT ssd (primary for the OS)
3TB Seagate HD (being accelerated. Formatted as 2TB and 1TB partition)
60GB OCZ Vertex 2 ssd (used to accelerate the HD)
All are formatted as NTFS. In Windows Disk Management, the 2TB HD partition appears as normal, the 1TB partition appears as "unallocated". If I disable the cache acceleration the 1TB partition reappears normally.
I upgraded to Intel RST 10.8, which was the latest provided from the manufacturer's website. I tried to install the more recent 12.x update directly from the Intel site, but that caused major issues (failed to boot up, had to restore to a previous config before those drivers). If this is a known issue that's been addressed between 10.8 and the latest 12.x, that info would be helpful - I will ping my motherboard manufacturer to provide a compatible Intel RST installer in that case
I was not able to replicate this issue. I had to initialize the mechanical drive as GPT since MBR only allows creating one 2TB partition; it was not possible to create a second partition from the remaining unallocated space. However, in GPT both partitions remained accessible with acceleration enabled or disabled. I guess it may help recreating the partitions again but I am not sure if you have such possibility.
Otherwise more information is necessary for further troubleshooting, would you kindly provide a copy of the IRST system report (Help, System Report, Save)?