@GM:
When you compile a mobi yourself with KG/KP 2, it produces a 'dual' mobi. A .mobi file with both a legacy mobi6 part, and a KF8 mobi8 part. When you view such a file on a legacy device, you see the mobi6 part, when you view it on a KF8 capable device, you see the mobi8 part. (The KP lets you chose which device you want to emulate).
(Enjoy the bajillion of different names used to describe the 'new' format: KF8, mobi7, mobi8, azw3... I usually go with mobi8 when talking about the internals, since it's the mimetype used by amazon for KF8 files (application/x-mobi8-ebook) and KF8 for the rest since it's the 'marketing' name).
When you convert a mobi via Calibre, you can choose what to do: a dual mobi, a mobi6, or a mobi8. Right now it's a tweak, in the next release (0.8.65) it'll be a setting in the mobi output plugin. It defaults to a single mobi6 part right now.
When you get a book from Amazon, they will automatically send you the *single* part adapted to the target device. Usually a mobi6 as a .azw file for legacy devices, or a mobi8 as a .azw3 file for latest gen devices.
And to get back to the OP's question: I've indeed seen a bunch of KF8 files from Amazon where the font size (among other things...) was slightly different than the 'older' mobi6 version I got on my K3. Nothing you can do about it, except strip it and tweak it, or strip it and convert it to mobi6. That's the joy of extended CSS capabilities: more chances for people to get it wrong.
Once simple way (for now) to check if you're reading a KF8 is to take notice of the line spacing. It's currently, let's say... 'broken' on FW 4.1.x/5.1.x, and forced at a slightly larger size than usual (on the lowest setting, it's still larger than the medium setting on a mobi6 file). [Although, in this specific case, since it depends a bit on the font size, that might not be the perfect example to check...
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