Nice that you discovered IrScrutinizer, but please update to the current version 1.1.1. Your version is almost a year old.
Can I use IrScrutinizer to help tell how my remote is sending multiple commands? When I hold down the up volume on the remote, the receiver has a very smooth and fast volume up,
yes you can. But we already know the commans the Yamaha is using for that, NEC1, D=122 (0X7A) F=26 (0x1A) (volume up), F=27 (0x1B) (volume down).
but when I send the command from my USB-UIRT it is pretty jerky.
When I send this signal using IrScrutinizer and any supported sending hardware to my Yamaha (RX-V1400 if that matters), it does the right thing. So, assuming you really (try to) send NEC1 and not NEC2, your sender, driver, or sending hardware is to blame.
I only have the USB-UIRT to capture IR commands.
IIRC, that HW does not capture the modulation frequency, just using a demodulating receiver, so it is not an ideal capturing. Which, BTW, is completely irrelevant if you are interesting only in, e.g., NEC codes with known modulation frequency. Nevertheless, supporting the USB-UIRT is on my wishlist, but not with the highest priority.