I have a SATA 2 drive which bencjmarks at about 110mbs write, and 125mbs read. A partition on the same drive runs at about 60mbs read and write. A SATA 3 drive connected to the same SATA controller runs at about 90mbs read and write.

I tried installing a SATA 3 controller in my system in the PCIe x1 slot but it doesn't appear to be running SATA 3 mode. Same 90mbs R/W performance as the SATA 2 controller.

The performance seems to be all over the place, and the SATA card I purchased doesn't work in two systems. I initially bought the SATA 3 card to upgrade a Dell XPS 420 with an Intel 520 120gb SSD. I yanked the card because there was a negative effect from the on-board sata 2. Yes, this system is supposed to be Rev 2 on the PCI, but the card isn't recognizing it. The other system is an HP 3130MT, and it didn't work in that one either. The card is an SY-PEX40039, sybusa or asmedia or iocrest. Can't reallu figure out who made it honestly.

Anyway, just trying to understand why the dependencies in performance.

I can see that you're trying to explain your questions, however (a) for performance issues much more detail of exact tests would be needed (as well as a clear explanation of which figures were your test results, and which were figures from other people's tests) if this subject was actually on-topic here, but (b) this subject isn't on-topic. Questions about compatibility between different SATA HBAs and different PCs are also not on-topic (that's not a disk repair or data recovery issue).

The best picture I can get from your story, is that you were expecting a SATA3 drive to be faster than a SATA2 drive, and are surprised when that isn't true. In short, using a SATA3 drive & controller will only produce an increase in throughput if the previous SATA2 component (replaced with one supporting SATA3) was actually the bottleneck. As far as I can see in your description, that wasn't the case, hence you saw no improvement. Therefore your bottleneck(s) is/are elsewhere. The challenge when trying any type of performance improvement, is to find the bottleneck. It isn't necessarily the interface.

I expect you'll get more help with this type of issue (and with your SATA HBA compatibility problems) in a PC-oriented forum Good luck!