Sounds like you are not using a 2 way tester. I have seen this before and it drove me nuts til I added the 2-way injector to my Pentascanner.

OK, what happened to me was that my crimper had gotten old and was not properly seating the pins. Looking straight on at the connector I could see some pins higher than others. This caused intermittent faults. Even the HD crimpers using swappable dies wear out if you use them enough. The cheaper ones are even worse as their rivet joints loosen up. Also, not every connector works in every crimper. I bought a bag of one brand that just did not fit my Paladin crimper. Some of those crimpers only take round cable connectors. Some only seem happy with flat. And if you have a swappable die model you have to be sure to use the right one. I run into no end of trouble with home made patch cords so I eschew them as a rule.