Question Graphics card working in pcie x4 but not x16

[Ki_Tso]

Hi, First I'm gonna tell you specs of old and current pc: (Also this is gonna be long, I'll try to mark the more important parts with Bolding)
Old(!) PC: {
--MB: Asus H97 Pro Gamer,
--CPU: Intel Core i5 4460,
--RAM: Kingston HyperX Fury 4GB DDR3 1866Mhz * 4,
--GPU: Asus Dual Gtx 1060 3GB,
--SSD: Samsung 850 Evo 500GB (sata),
--PSU: Thermaltake Smar SE 630w
}
Current(Upgraded) PC: {
--MB: Gigabyte B450M DS3H,
--CPU: AMD Ryzen 5 2600x,
--RAM: Kingston HyperX Fury 8GB DDR4 3000Mhz * 2,
--GPU: (Same as above),
--SSD: (Same as above),
--PSU: (Same as above)
}
Now to the problem, 1 year ago I bought new cpu/mb/ram (I bought an Asus Prime B450M-A(CSM) back then), installed everything and ready to go but my mb beeped in a certain pattern which I then realized it meant it had gpu problems, I then sent the mb to warranty company, after a week they said it was some bios problem and now it's fixed, brought home the "fixed" mb, tested it, but still didn't work so I moved everything back to old pc (Because I needed(!) to continue playing games)
About 8 months ago me and my uncle(he has some computer knowledge) went through testing it again, I don't remember what we tested exactly, but probably every basic problem solving method, There existed a weird problem, my 1060 worked fine on the h97 mb, but when I connected it to the Asus B450M-A mb it didn't even post, even keyboard's numpad(trying to turn it on) didn't work, I connected a 9500 gt graphics(Which I believe is full length but uses pcie 2 8x) card to the mb and it worked fine (weird) .1 month ago I even tested connecting 2 PSUs(630w + 500w) at the same time to upgraded pc ( 500w to cpu and mb, 630w to gpu), problem insisted except time time keyboard was working!.
Yesterday I bought the Gigabyte mb because I was pretty sure it was mb's fault. Previous Asus B450M mb had only 1 pcie 3 16x, the new one has 1 pcie 3 16x and 1 full length pcie 4x, more room for testing.I said to myself "Ah sht, here we go again" and started changing mb ... same problem, so I moved the graphics card to the lower pcie 4x slot, aaaand it worked (However I couldn't connect most pin-related stuff to mb because the gpu was covering them, I had to power on the pc by using a very thin screw driver :S ). I also updated new mb's bios and gpu's bios(!). So here's my "Question", why does my graphics card works on the old h97 pcie 3 16x and on the new Gigabyte's pcie 4x but not on neither Gigabyte nor Asus(new one) pcie 3 16x slots(Not working: no display)?
P.S. Here's extra hardware I have access to: {
Geforce 9500 gt, Geforce 7100 gs(!), 500w psu, Samsung 128gb sata ssd, 2 sata hdd
}
P.S. My 500gb ssd has Debian 10 on it(The one I'm currently using(and writing this post on it)), and the 128gb has Windows 10.

Thank you in advance. 💙

 

[Vyrvelata]

Welcome!
Well that is some weird problem...
It's sounds like there is some incompatibility or some sort of a problem with the slot of the card, maybe one of the connections is somehow compromised but it's not affecting your Intel mobo.
I would've asked why don't you use it on the second PCI-E x4 (full slot), but you already answer that... I was thinking it might not to be that awful (you will loose performance for sure) in terms of bottleneck.
Well for a start my only idea for now is to try PCI-E Extender, even if it continues not working on the main (you should try) PCI-E slot...It will work on the second one and you will be able to connect everything you need to. I hope some will join the conversation to help as well.

 

[Ki_Tso]

Welcome!
Well that is some weird problem...
... conversation to help as well.

(Sorry about cutting your message, didn't want the reply to be big and take the whole screen!)
Thank you for replying, I will try to find a pcie extender to test this out, I could try to go to a local computer repair store to see if they can find a better solution(Than using x4), but beside them having more hardware to test on my computer I kinda doubt it since I live in a small city...
I can live with a slightly under utilized 1060, but I really need to find out what the problem is, for me to be able to live-on.