I did an alignment on my unit
Does this mean the radio's counter reads differently from an external counter? L22, L23 and L59 each sets the radio's frequency with the clarifier centered.
L59 sets that frequency in USB to match the other two modes.
Is L59 going all the way to one end of travel without putting the radio on frequency?
Just not getting the picture of when the counter is reading wrong. If the radio's clarifier has been "expanded" to cover a wider range than the stock setup, this can make it harder to make L22, L23 and L59 all set properly.
If the Coarse clarifier knob now covers a whole 10 kHz channel or more when turned end-to-end, you can't make the channel center frequency come out right with the pointer at 12 o'clock any more. Turn the Coarse knob's pointer to 3 o'clock and see if L59 sets properly now. Odds are you'll have at least 1.5 kHz of range turning it all the way to the right from 3 o'clock, and a whole channel down at around 9 o'clock.
If you really want to see the channel center frequency at 12 o'clock you might have to "un-stretch" the clarifier's tuning range.
Naturally there are dozens of ways to set up or mangle this radio's clarifier setup, so your mileage may vary.
A lot.
73