The inputs on a 200S are just like many of the classic Fenders....the # 2 input has 3dB less gain than the #1 input.
If you plug into input # 1 the 1M to ground comes first, with the 68k connected to the grid. If you plug into input # 2, the signal goes through the first 68k resistor to the tube's grid. With nothing plugged into input jack # 1, its 1M resistor is shorted out and its 68k resistor is connected to ground. This is the same as a 136k pot turned down to the 68k point, or halfway off. This loses half the input signal, or a 3dB loss. If you plug in two instruments, one into each jack, then the 1M resistor is back in circuit and both inputs revert to full gain.
If you plug into input # 1, there is a 1M input impedance. If you plug into input # 2, there is a 68k input impedance. The 68k input impedance loads down the output of the pickup more than the 1M impedance does, and the pickup will react to different input impedances differently too since it is a reactive device. So it makes perfect sense to me why the tone would change if you plug into one input or another input. The low gain input has always sounded dull to me in comparison to the high gain input, probably because there are less highs. Its the same kind of thing when matching up a microphone to a preamp...especially with ribbon mics. Many of them are very low gain and they need a boost, but the input impedance of the mic preamp can make or break the sound of the whole system. That is why the better makers put a variable input impedance in their mic preamps.
Greg