If you are unsure if your hardware works, best to move your x1/x16 adapter and your graphics card to a desktop PC and actually test that your hardware indeed works
Try the adapter and card in the x16 slot of a desktop as well as the 1x slot of the same desktop as this will/may highlight some issues.
And it would be even more relevant if you have access to an MSI desktop using a similar generation of hardware/bios as your results should be directly transferable to the MSI J1900 motherboard.
You may have to lean on a friend if you don't have a 'normal' desktop to use for such tests...
Note, a quick look at the
MSI JI900 details specs page indicated the PCIe slot is version 2.0.
Hopefully the graphics card you purchased is PCIe 2.0 compliant (though i doubt this is the cause).
Unfortunately further down the details specs page, there is cryptic comment stating:
MSI Reminds You...
• The graphic output can only work with CPUs with GPUs core inside.
But i'm not sure what relevance this above comment has as the CPU is soldered on the board so it's a "you get what you get" with respect to CPU graphics.
So does MSI really mean that the BIOS has locked down the graphics subsystem and as such BIOS will not allow you to disable the integrated graphics?
Which brings me to the question, does the BIOS have an option to disable integrated graphics?
If there is no BIOS option to disable integrated graphicst, then you may have issues as the PCIe graphics may simply not work (or work oddly?) while the integrated graphics is still trying to do its thing...
So forcing the lane count using a wire may not help (as i mentioned earlier) nbut as it's simple to do, try placing the wire on the x16 side of your adapter (where the graphics card plugs in) and see if that helps.
If not, then try placing it on the motherboard x1 connector (where the adapter plugs in) and see if that helps.
I don't think it would be wise to place it on both sides of the adapter but who knows in such situations...
In reality, i suspect it's the motherboard BIOS that is the issue in which case buying another graphics card may not help to solve the problem.