Check what GPU-z shows while the card is under heavy load, the speed should jump to PCIe 2.0.
Now it is impossible to know what we exactly saw it's too late.
Can't flash back to original bios because the management engine as part of the bios is blacklisted.
Now 2.5GT/s could mean 2.5 giga transfers, of what? As we know the PCIe sends information much like the DDR memory, the effective bandwidth is doubled, to 5GT/s, but was that number doubled to begin with. Or the card could be idle. Or we saw 2.5 originally but as there is so much distance between the "2" and the ".5" it looked like 5GT/s.
I also looked before and after flashing the new bios, and remember the 5GT/s then it wasn't anymore. I could clearly remember now that it was 5GT/s, I remember thinking how happy I was to see the correct speed detected, but it could be false memory that I just created on top of what really happened, but I'm pretty sure it was 5GT/s.