I doubt they're making "upgrades". More likely it's just normal unit-to-unit variation or perhaps slight changes somewhere on the manufacturing line -- new solder supplier, for example, or in the case of Philips a whole new manufacturing line (China vs Mexico). Variation in headphones between different "batches" is hardly new and neither is variation between individual units made around the same time. The more complex the device, the more likely there will be minor differences between units (especially if there's any "hand-made" element to them... just ask Beyerdynamic owners!). I suspect everything from wire and solder quality to diaphragm uniformity and glue distribution could be slightly different in headphone units. It's just with headphones we're more likely to hear those differences than with other electronic products. Sometimes you see the differences -- in the photography world there is often-considerable variation between lenses of the same model, for example.
The point with manufacturing these things is not to get every unit absolutely identical, but to get every unit within an acceptable range. So, yes, I expect that whatever the headphone if you were to buy two copies and compare you might well find slight differences in the sound. In the photography world it's not unusual for people to buy 2-3 copies of a lens, test them all, and keep only the sharpest.