Wow, that's an interesting observation!
Personally, I'd first check with a more spherical molecule if the effect appears too. A sugar maybe, or adamantane etc, depending on the solvents used for the polymers. And also with the solvents alone if their viscosity is measurable.
Then, check at constant temperatures if the viscosity evolves over a longer time.
Conformation, yes... Or maybe the polymer isn't fully dissolved during the first measurements. If it's dissolved as pairs of parallel strands, it will deform less easily than single strands. Or the macromolecule stays packed by intramolecular van der Waals' forces for some time, and the solvent takes times and heat to unfold it.
The flow itself may stretch and orient the macromolecules.
In most technical polymers, the molecules are already stretched and oriented, purposely in fibers and films, unwantedly at injected parts.
Polyglycols serve to improve the viscosity index of lubricating oils as heat unfolds them. Similar effects should happen with POM-C and others. Does this take time? Or is there hysteresis in the temperature effect?