I am listening from the same headphones, playing and recording, then listening to the recording.. so only difference I see here is the output of the USB vs output of the headphones. I think I should try recording from a DI interface.
The headphone output frequency response is flat. The OP is probably having his ears play tricks on him since when he's recording he's getting some bone conduction from the guitar itself. As bone conduction is biased towards low frequencies this will give the impression that the sound isn't as bright. On playback it's just the recorded signal.
People have the same experience recording their own voice. You are used to hearing the resonance of your body mixed with the input of your ears. On playback its easy to think your voice hasn't been recorded accurately.
Not sure this was perfect, but I did a little experiment tonight where I recorded output1 and the headphone output at the same time for comparison. I just took a Y cable I had with two 1/4 mono jacks running into a stereo mini plug at the other end. Plugged one 1/4 cable into output1 L, and the other into the headphone output (which is plugging a mono cable into a stereo jack, but you just get one channel). So this puts the output1 signal on one side of the mini lug and the headphone signal on the other side of the mini plug. I put the mini plug into the line in jack of a simple handheld portable MP3 recorder. I used a simple mono amp/cab patch with cab sims on and made a recording while noodling around. On playback, the left and right channels sounded the same panning between them, which seems to indicate that the signals sound the same, at least when they're flowing into the same device.I wish I could record the headphones out..
Not sure this was perfect, but I did a little experiment tonight where I recorded output1 and the headphone output at the same time for comparison. I just took a Y cable I had with two 1/4 mono jacks running into a stereo mini plug at the other end. Plugged one 1/4 cable into output1 L, and the other into the headphone output (which is plugging a mono cable into a stereo jack, but you just get one channel). So this puts the output1 signal on one side of the mini lug and the headphone signal on the other side of the mini plug. I put the mini plug into the line in jack of a simple handheld portable MP3 recorder. I used a simple mono amp/cab patch with cab sims on and made a recording while noodling around. On playback, the left and right channels sounded the same panning between them, which seems to indicate that the signals sound the same, at least when they're flowing into the same device.