Hi, I had a similar (but not the same) font-sizing issue related not to the version of Pd, but the version of linux I was using. Not sure if it will help, but the problem along with the workaround solution I found is described in this thread:
BTW -- there was some clarification on the Pd list as far as exactly how those font startup flags are supposed to work. The -font-size flag is different than the -font-face and -font-weight flags in that while the latter two flags will affect all patches opened after Pd starts, the -font-size flag will only affect the default font size applied to newly created patches. Supposedly this is because the font size is the only parameter out of the three that is actually stored in the patch. Personally I still find it to be a glaring inconsistency, especially since this is not explicitly stated in the help file. Nonetheless, this is how it's supposed to work.
Keep in mind that specifying font face or weight will also affect the sizing and spacing so if you specify either of those two variables along with -font-size it may appear that -font-size is having an effect on previously created patches when it is actually the other variables causing the change.