If your craft beer is unfiltered, unpasteurised beer with live yeast, then any kind of transport could alter its flavour profile.
Other variables that could effect its flavour are:
- changes in altitude (not during flight)
- no resting after transport (depending on yeast content up to two weeks)
- bottling problems (oxygen in bottleneck)
- difference between drinking and ambient temperature (e.g. beers taste different in summer and winter)
- olfactory changes (flu, humidity, ambient smells)
- drinking method (glass or bottle make a taste difference)
- transporting bottles that are not so fresh (closer to their exp. date)
- cosmic radiation
- altitude changes during flight irreversible
Any of the above mentioned changes in temperature as well as choosing a glass instead of a bottle etc. effect CO² in various ways. This results in a different drinking sensation (the tingling in the nose; try "smelling" the CO² and compare with a flat beer) and different taste (pH).
Humidity, climate, season could alter your perception. An imperial stout for instance takes you over the edge in summer while you would feel perfectly fine in winter.
Ambient temperature has an immense effect on the beer. It effects nearly everything from how much CO² is released upon opening the bottles to what the perfect drinking temperature is. The drinking temperature has an immense effect on how strong hops, sugars and alcohol taste.
Such changes in taste are not unheard of and more likely to occur in strong, malty beers. Flights are not necessary to have such an effect. Any long-distance transport would do.
To test if the beer has actually changed during transport, you could try transporting it back.