A CE-680 flight crew failed to meet a crossing restriction when the FMS appeared to have unilaterally altered their programming of the restriction.

Narrative

Los Angles Center gave us a ZZZ1 crossing restriction of FL240 but later amended the restriction to cross ZZZ1 at FL230 or below and to maintain FL200. The flying pilot put FL200 with the altitude selector. We both saw and confirmed and pointed at the newly selected altitude in the Primary Flight Display (PFD). Then the flying pilot put in the flight management system the wrong altitude of 2;300 Below at ZZZ1. I quickly corrected him and the pilot flying put in FL230B. We were 15 miles from ZZZ1 at FL250; the restriction was no problem. Here is where it gets it gets crazy (busy and distracted). I later looked down we were 10 miles past ZZZ1 at FL234. The altitude selected in the PFD showed 21;300. It had changed by itself! I can only guess it changed when we entered the wrong altitude in the FMS. We are using the Honeywell Primus Epic FMS with phase 5 [software]. Our company is taking out phase 5 and going back to phase 4. For example phase 5 has restrictions that we can't fly a coupled approach below 800 FT because of nose tuck under incidents. Phase 5 can't be trusted and needs to be off the CE680.