I have my PF2000 setting at "0". I have entered individual trans altitudes for the various areas in the PFE page for transition altitudes. This works for me. What do you have Italy set to in PFE ?
Also check your SIDS/STARS page for LIPZ. I think (only think) that a different setting on that page might override the general settings.
The transition level for Italy is 6,000ft. That was set and an x put in the transition level page in PFE and 6,000 put also in PF2000.
The SID I set up for LIPZ finishes at FL140. It was all working ok until I ran makerwys earlier. PFE then forgot other SIDS even though they were listed and they had to be resaved. So I don't know what happened.