Hey cK - Juniper does NOT recommend upgrading to 6.5R1 from anything prior to 6.1R1. I would recommend doing a multi-step upgrade to be on the safe (with a full backup of my configs of course before starting).
I have found that there can be issues when performing major jumps and 5.5 to 6.5 is gigantic.
going from 5.5R7 (build 13237) to 6.3r6.1_b14715 can this be performed in one shot?
upgraded this weekend from 5.5 to 6.4 (via 6.3) without problems