Maybe he was confused by two similar terms. In the manual, Yamaha uses "up-conversion" to mean analog to HDMI conversion (which can be scaled or not), and they use "up-scaling" specifically to mean converting from SD to HD resolution.
In the feature list for the 6290 (1900) you'll see "Analog video up-scaling", while the 3900 has "Analog and HDMI video up-scaling".
But your problem of the PVR resolution being changed sounds like the bug that's currently affecting all the new models (1900/3900/Z7). Yamaha may come up with a fix for that eventually.