Can't say I have - only issue I ever remember was down to Compaq (the twist / no twist thing) which was an easy fix.

I've used single commercial flat, round & ones I've crimped myself without issue - any more details on the hardware (boards & floppy brands / models)

I am a bit confused by your reference to 40-pin floppy cables .

PC floppy cables have 34 pins on the controller side, not 40 . The connector meant for a 3 1/2" drive is also 34 pins . Additionally, AFAIK, there should be a twist in the cable and the primary floppy drive should be connected after the twist, even if there is only one drive on the cable . If there is no twist in a cable, I believe you would need to set jumpers or DIP switches on the drive to let it work as primary drive but, again AFAIK, most 3 1/2" drives do not have such jumpers or DIP switches, so you must rely on the twist in the cable . This is retrieved from my very long-term memory, so you may want to double-check all this .

Here is an example of a floppy cable with a twist : https://www.amazon.com/CAB-FDDS19-4PK-Univers … n/dp/B07Z9WVPYP

Sorry, I wasnt thinking when I posted....it is a 34 Pin Floppy cable........

The cable has the twist in it, both of them do....not sure what is up....its multiple boards and multiple floppy drives as well.....

If it has a twist before cable end have not had an issue, except as PC Hoarder Patrol said about some Compaq motherboards which require a straight cable to A: and only support one floppy drive.
added: Have some older early 90's 3.5" 1.44Mb that have had issues with some cables but cannot remember if those were single drive drive or dual drive cables....

Smack2k wrote on 2021-02-06, 02:26:

Sorry, I wasnt thinking when I posted....it is a 34 Pin Floppy cable........

The cable has the twist in it, both of them do....not sure what is up....its multiple boards and multiple floppy drives as well.....

A twist at both ends is not right. Biff it and use another one.

Smack2k wrote on 2021-02-06, 02:26:

Sorry, I wasnt thinking when I posted....it is a 34 Pin Floppy cable........

The cable has the twist in it, both of them do....not sure what is up....its multiple boards and multiple floppy drives as well.....

Are you aware that there is not just two possibilities to orient the cable, but four? Not only you can have the connector on the drive inserted 180 degrees rotated, but you also can have the twist on the wrong side. Try turning around both connectors, if you didn't already. The twist must be near the actual pins 1/2, not near the actual pins 33/34.

OK, the twisted side of the cable goes on the drive and red wire should go to pin 1 on the motherboard and on the drive, and the wire should be twisted only on the side of the drive of course. This applies to the 99,9% of the cases at least. Wath out for cables that are keyed and may be wrong, or cables that are not keyed.

I meant both cables I've tested have twists in them. I know the twist goes in the floppy drive side. I've tried them various ways with no luck.....maybe the cables are both just bad.....turned them around.....

Im guess bad cables...