Help! SSD/Windows misbehaving

[Daichin]

So I just got in, turned my computer on. Half an hour later it boots up. My computer has a 60gb Vertex 2 drive installed and generally takes no longer than a minute or so to boot.

AHCI is on.
Windows install is a month or so old.
SSD is only a month or so old.

I'll be honest, It didn't actually seem lightning fast when I first in installed.

Here is the results of a crystaldisk benchmark that I just ran. Seems both really low and really odd.

Any insights appreciated.

EDIT: Apologies for posting in the wrong forum, I totally forgot about the Storage Drives section.
Thanks!

 

[Daichin]

1. Windows 7
2. About 20% yeah, but it was more full the other day and it was much faster than it is now.
3. How do I find this out?
4. DFI 790FXB-M2RSH - Four SATA ports are populated - 2 for mechanical drives, 1 for the SSD and one that isn't plugged into anything (it hasn't been for months, it's for the optical drive when I occasionally use it).
5. I ran the windows performance test. Indexing is off, TRIM is enabled etc.
6. When I first installed it I ran a benchmark to ensure it was working but didn't really look at the numbers all too much and haven't benchmarked it since.

 

[Daichin]

3. Firmware is 1.35.
2. Done this.
4. It says "pciide - BAD" and "103424 K - OK"
Why would this have happened? I'm certain it's set to AHCI in the bios but the only drive that is reading as AHCI is an ancient 320gb mechanical drive.
EDIT: Is it likely this is because my motherboard has a limited number of AHCI ports?