Which version of NPAPI Flash Player is installed in your machine? Could you add SilentAutoUpdateVerboseLogging=1 in mms.cfg file and try triggering the update service on your own. For the same, if you are using 64 bit win 7 go to C:\Windows\SysWOW64\Macromed\Flash and run the FlashPlayerUpdateService present in the folder as administrator. If the machine is 32-bit you will find the update service at location C:\Windows\System32\Macromed\Flash.
Before running the update service delete the FlashInstall.log file present at the same location as update service. Once you have run the update service, share the FlashInstall.log generated. To share the file you can go through How to share a document . Once you have uploaded the log file please share the link to the log file here.
Thank you for your extensive reply. I left the computer on and logged in to give it some time and I just checked now, the NPAPI pluggin is also updated now without any interaction from me needed. So I guess problem solved
Silent AutoUpdate updates Flash Player ActiveX first and then when it runs again (about an hour later) it'll update the NPAPI plugin. It's possible you checked prior to the one hour time-frame had lapsed. If you see it take more than one hour to update the NPAPI plugin after the ActiveX Control has been updated there may be an issue with the system and we could investigate further with verbose logging enabled to capture the Silent AutoUpdate activity.