As someone who has been crimping Category cable since well before V5 was released, only recently did I finally have the chance to try crimping V5 cables.
What I can say beyond a shadow of a doubt is that VEX’s crimping tool, with a plastic die, is utter garbage. I had several failed crimps, causing the Brain to simply not recognize connected motors. When I did a sanity check with a crimping tool I used for actual Category cabling (with a metal die, just like every crimping tool worth anything), every single crimp worked (and yes, I used the exact same technique).
So, for all I know, the incidence of issues with custom-crimped cables but not factory-crimped cables could somehow be related to the crimping tool. Your mileage may vary, but I can confidently recommend even this $10 crimping tool over VEX’s. You can even get a whole crimping kit, complete with cable tester, for less than the price of VEX’s crimping tool (I can confirm the crimping tool in this exact kit worked perfectly on V5 cable).
TL;DR Try using a real crimping tool in the future. Testing your cables with a cable tester before use is a good idea too.