A B747-400 First Officer reported the aircraft refused to climb to the altitude requested by the commercial flight planning service flight plan. [He] stated the climb ceased; the autopilot disconnected; and the FMA annunciators indicated mode faults. After leaving the area of turbulence in which this event occurred the climb was accomplished without incident.

Narrative

On a long range transpacific flight; during an en-route flight plan directed climb to FL350; we encountered moderate turbulence. Our autopilot refused to climb above FL344 [and] the autopilot disengaged. The FMAs that were previously engaged; 'SPD' and 'VNAVPATH;' were lined through with warning yellow lines and an alert signal sounded. Captain was pilot flying and re-engaged the FMAs in 'SPD' and 'VertSpd.' Our red stall indicators were collapsed to 240-315 KTS. Our yellow stall warning indices collapsed to 278-308 KTS; +/-15 KTS stall margin. KIAS was 293 KTS. While the moderate turbulence continued; we leveled off at FL344 and sped up to .858-.862 mach. After about 4-6 minutes the moderate turbulence ceased and the climb was continued to FL350. The yellow buffet indicators remained at +/-15 KTS. This climb occurred at a location where we were to cross the forecast jet core (90+ cross winds). Upon checking the buffet chart we had a 1.2G protection margin. The moderate turbulence at that location led us to believe we were maximizing the performance of our aircraft.It should be noted that another climb to FL370 later in the flight would have presented us with a similar situation. We would have been in a condition with a 1.2G buffet protection margin while crossing the jet again; but this time with a 140 KT crosswind. We chose not to climb until lighter and past the forecast jet crossing. This flight was planned to cross the jet core three times over the Pacific. It is also important to remind ourselves that we are building a core of pilots that are being trained to not believe the performance numbers our FMC presents to us. While the 747 pilots have been provided an 'adjustment factor table' for the differences between the older engine and the now 10+ year old 'phase 3' engines; it only corrects for thrust; not optimal altitude; max altitude or other tactical information.Since a decision has apparently been made to ignore the mismatch between our commercially prepared optimized flight plan performance and our aircraft's FMC database; I predict these episodes will continue to be experienced by crew -- some experienced crew and some not. It is imperative we immediately initiate a system upgrade on our 747-400; the 757 winglet; and the upcoming 767 winglet aircraft's FMC and aircraft performance databases. Our FMC computed maximum altitude was FL359 during this incident. After flying this commercial flight planning service for three years; I am very suspect of what the aircraft will do during maximizing conditions. After this experience there is no question about our need to update our aircraft's database immediately. If safety is truly important to us; there can be no question as to what we need to do at this point. Do we really want our pilots doubting the FMC's calculations?It appears that the aircraft software performance database did not want to perform to command under moderate turbulence conditions. This is not necessarily a commercial flight planning problem; this is an aircraft software and database issue that was unknown prior to the receipt of the phase 3 performance data tables. Prior to [the current flight planning service] the aircraft was not dispatched with the more optimal performance database; hence the old calculations more matched our FMC's output. Confidence and confusion of which information to use is now an issue. Several revisions to our commercial flight planning service have occurred. The pilots are not informed of the contents of these changes in the calculations of his commercial flight plan. A publication notice should be published immediately to inform our captains of what they are signing for in our releases. Every software upgrade and or revision of changes should be placed in our handbook. The 400's FMC database is mismatched; as will be the 757 and 767 winglet aircraft. It will take corporate senior executive attention to resolve this issue with Honeywell and Boeing. Risk management is essential to control this in the future.