Was thinking about it a bit more and maybe you started the program with too high a weight? On your 5/3/1 setup did you set your 5 rep week to be the same as your previous programs 5 rep weight. Andy says in the program PDF:
The main thing is to not start too heavy and start missing reps on the first 1 or 2 cycles. It might take you a cycle to get through all the rep ranges and then you can go and tweak everything for cycle 2 if anything was either way too easy or way too hard.
Since I am doing an 8/5/2 rep rotation I set the first cycle's 2 rep week weights to be roughly my last cycle's weight on the main lifts. Some of them were 3x5 and some were 1x5 with back off sets. I was coming off a once a week increase on an Andy-inspired HLM program. That let my 8 rep and 5 rep weeks be a little lighter as he lays out in the program. It was a bit of a deload going into the new program.