Same boat with me as an electrician/instrumentation mechanic.
I deal with magnetic flux all day long (it's what electricity is - in a sense). For the most part, magnetic fields DON'T cause too many problems for most people. In fact, for 99.998% of people, magnetic fields DON'T do anything. There is however, a VERY small population that is extremely sensitive to magnetic fields. They develop headaches and other nervous system 'problems'.
Magnetic flux lines (magnetic fields). And their interactions cause various effects. Paralell fields attract or repel based off of the fields polarity. Fields at right angles generate electrical charges...
So some with a cyberarm that passes through a field MAY register an increased electrical charge in there system of....... a billionth of volt. (Egen = BLV).
If he is waking next to a magnetic source, he may experience a "pulling or pushing" sensation of a few milli ounces...
After all it's the two fields interacting. The mag field of his body and cyberware VS the other field source. Chances are his personal field is not strong enough to remain independent, and becomes integrated into the stronger field while in paralell... which doesn't do much as the field strength isn't enough to matter.
Now if we are talking seriously HIGH levels of flux, then you have an issue, as high levels of flux are toxic to living tissue. (But can do some spooky things! Like levitation of organic matter, slow the rate of falling of non magnetic objects, and other awesome, spooky things!). But you are not finding these sources of flux anywhere outside of super specialist labs and testing facilities. (The man made magnets capable of this are electro magnets, they take 18 to 24 months to build by hand, require the power of a city to operate, and burn out after a dozen uses.)