Another data point for you: I just updated a 3.3r installation to 3.3s.
Saw this line in pt3inst.log:
protop.pf already exists in etc, saving a copy as /opt/protop/etc/protop.pf.04.19
The new protop.pf does contain -inp 16384. So it looks like all is well with pt3upd.sh.
This is almost always for one of these reasons:
The -tablerangesize or -indexrangesize parameters are not set to cover the active tables & indexes. The ChUI "T" command will show you what values are recommended and create a sample .pf file for you in the ProTop temp directory. Unfortunately you cannot change these values online. A db restart will be needed.
The activity on the tables and indexes does not meet the threshold criteria. You can review the thresholds on the portal "Resource" screen. For development and test environments you probably want very low values. For Production you want higher values -- a chart with 2,000 objects on it will be unusable (that is why we have a minimum activity threshold).
You should also verify that etc/pt3agent*.cfg has the TableActivity and IndexActivity data collectors enabled. If they are missing from ptInitDC then that data is not being sent to the portal.