Yes, those fluctuations are not good news. Is it the same axises that is acting up in both runs? (tip: the nevest 1.05 QGCwidget has color legend in the logviewer).
It looks to me like the noise is very similar on both axises affected, indicating it comes from the same source. Apart from it beeing problems with the X/Y mag itself, sources of such noise could be the power wire to the battery running too close to the mags or noise coming from the uSD card reader circuit.
uSD card operation can use a substantial amount of power and can also be a source of noise in the rest of the circuit. It depends also on the class and size of the card. Higher speed and size usually means more power, and manufactorers specs vary greatly. Sandisk list max 200mA for write operation @ 3.3V, in 50 Mhz mode but that may be outdated, since the product manual was last updated in 2007:
http://www.altec-computersysteme.com/do ... M_v2.2.pdfSection 2.1
If this is actually true, we may be pushing the 150mA LDO that is supplying the uSD circuit. I have never used bigger than 8GB/C10 or seen this problem myself, but the earlier post about board not booting with a 32GB card could maybe be explained with that card drawing too much power...but its a guess, I dont have any facts to back it up, or a 32GB card to try out.
We also know that uSD card thickness vary greatly between manufactorers (I have seen from 0.65mm up to 0.82 mm). This means that thinner (<0.70mm) cards can have poor contact with the terminals, and in theory also increase power consumption. If you have a very thin card, it can be a good idea to glue a piece of thin plastic (tape) to the logo side to make it 0.75 - 0.8 mm thick. This will make it lock better into the slot and give better contact.
I guess what I am saying is, that you should try another card, and look at your wiring...just to make sure the noise is not coming from there.