Here is something to check.
Press and hold the VIEW button to bring up the system setup options. Use the right nav button to go to page 4 "outputs". To get the best sound when recording through USB, be sure the output is set to Studio/Direct. If it is set to one of the combo or stack options, the 500x will sound strange through your computer.
Likewise, when you hook it back up to your amp, be sure to set this option back to to the Combo or Stack option for whatever type of amp you are using, because Studio/Direct setting might sound strange through your guitar amp as well. Hope this helps!
Cheers!