I'm a bit lost. In both examples you have penalty for the same number of cities, just different of puppets which SHOULD NOT matter. What is the value "updated" with? The only case I could think of is that there was some bug earlier and now the game recalculates everything and updates the proper value. Example 1 you mentioned might refer to the variable MaxNumberOfCities (or something like that). The science penalty was used to be calculated in Civ5 based on this variable which is the highest number of non-puppeted cities you ever had at any time. So, if you have 5 cities and lose 1, you have 4 cities, but the MNOC remains 5. If you then found or annex another city, you go back to 5, which does not increase your MNOC and therefore does not increase tech penalty either. But it has nothing to do with puppets which should not count to MNOC and/or tech penalty! This looks like a bug to me.