Perhaps it's psychological - that heating over a stove has different emotional connotations?

An electric kettle often contains a build up of ..um, stuff?.. that could change the taste of the water.

Also, an electric kettle boils water more quickly, and perhaps reaches a higher temperature, which will then affect how well instant coffee dissolves and the precise make up of the coffee.

I've wondered the same thing because I have a stainless steel kettle which I use only occasionally on the hob and it always makes my tea taste odd. However, if I use it a few times in succession everything returns to normal. I decided that the steel must add something to the water, but once it's been boiled off it is no longer there to be added in sufficient quantities to taste. A kettle is normally in use several times a day, so reaches a constant state where it neither adds anything to, nor takes anything from, the water inside it. The most likely added substance, I guess, is a tiny quantity of metal oxide.

Gas has a smell.  Taste is really mainly smell.  So my guess is that the gas, which is highly volatile, affects the coffee - boiling water would incorporate air.  Whereas in an enclosed kettle, the steam condensing on the top surface of the kettle would drop back into the water, carrying some metal molecules with it.

When I boil water  in an open spout kettle over a wood fire the tea tastes of phenol from the wood smoke. Methane gas  is odourless but smelly thiols called mercaptans are added to tell of a leak. Perhaps these odours are infusing your coffee. Try again by covering the pan with a tight lid.