Seems like I found the culprit (or rather a solution) to this problem.I have exactly the same problem arising just last few days ago I was using it. N3DS is on GW emuNAND 9.5 and I always first patch the system (using the version 0.5 app and pressing START) and then switch on wireless (and switch off wireless before poweing off). This has been the case for like a month with no issues. Until recently what happened that when I exited Mii plaza application (pressing HOME) while it got suspended that update popup came up. I clearly remember going in and out of eShop several times in that session and going to Miiverse several times (which means the eShop spoof kept working), however this one day when exiting out Mii plaza app this is the first time I saw the update nag (the update got downloaded and asked to install it).
I was getting this message randomly on booting into GW mode: "You must update the system before this software or update data..."
Which tells that some application is forcing the system to be updated (meaning the system update itself hasn't downloaded yet).
Since I was experiencing this problem after exiting Mii Plaza, I went into Data Management in Settings app.
There, in Add-on Content section I found two of Mii Plaza data, one was only 2 blocks and other which clearly saying Mii Plaza Update and was 430-ish blocks something.
After deleting just that Mii Plaza Update I did few boots into GW mode and so far not having any such update nags again
TL.DR: If you are getting update nag like this: "You must update the system before this software or update data..."
Then try remembering what last application you were using when this start showing up, go in Data Management >> 3DS Software >> Add-on Content, find and delete that.
FreeMultiPatcher seems to be doing its job fine (not letting it download the system update). It's rather some application itself got updated. Hope this helps
Last edited by Just3DS,