I found after a year on 5-3-1 that I was having problems with 1RM's. It appeared that after so long of working on rep strength, my CNS was not quite used to handling maximal weights. I failed a bunch of times, especially on bench. What seemed to help me through it was a 6 week run on Thibideau's HP Mass, where you are essentially working a ton with your 3 RM's. This seemed to help carry over with my 1RM significantly.
A better solution though may have been to implement 5-3-1 for Powerlifting, where you work up to heavy singles in the 3's and 5-3-1's weeks (after switching the 3's and 5's weeks around). This would allow a lot of rep work, as well as circa ME work as well.