This sounds familiar. How did you determine SATA 1 vs 2? What OS are you using? Do not dismiss this issue and if you can't access the ME to provide Acer more information, get them to deal with it. It sounds like you are implementing RAID that isn't original so they may say you have voided the warranty however. Now that I think about it, I believe Port 0 is treated differently.
I determined SATA 1 vs 2 using the Intel Storage Manager software, which was bundled with the PC. I finally convinced them to replace the motherboard, however, the password issue with ME exists with the new board as well. I haven't installed the Storage Manager software as of yet, as I'm trying to keep things as simple and clean as possible.
Port 0 did register as SATA 2. With six ports and integrated RAID, I can't imagine that's the only port that would support SATA 2.