Re: Strange PCIe problem.
1.
You say the card works the first time after installing software. Perhaps an updated version of software has come out. Have you checked whether you have the most recent version?
2.
Apparently the software leaves the card in an unreadable state after use. Is there any command/ routine/ setting/ option, etc., that could switch off current flow in the power lines on the card?
3.
Since the card works occasionally, it's not likely the contacts are dirty. Nevertheless you have an intermittent problem, and if there is dirt or tarnish present, it can prevent a good electrical connection, and the card may not be detected every time.
Before you do the following steps, you should attach a wire from yourself to an electrical ground, so that you have no static charge on you. Or at least touch a ground to discharge static from you, before you handle the card.
Remove the card from the computer. Rub a pencil eraser across the contacts until you can see clean metal surfaces, with no dirt or tarnish.
A rubber pencil eraser is commonly recommended. Sandpaper or steel wool are too coarse.
Looking with a magnifying glass, clean away all bits of eraser residue. Install the card and remove it again.
Examine the metal strips for any dirt or tarnish that was picked up from the contacts inside the computer.
Rub the card contacts with the eraser again.
Install the card, remove it again, examine for dirt.
By repeating these steps you are hoping to clean the contacts inside the computer, and on the card. The goal is to create a good electrical connection.
When installing the card, make sure its pins are fully seated in the computer.
4.
Sometimes it helps to unplug power from the computer for 30 seconds, to let all circuits fall back to zero.