Well not so much the size as the voicing. Getting a very middy speaker on a very middy amp with mids on the EQ quite high will lead to the amp sounding "boxy".
It could be the position of the speaker thats emphasising certain frequencies. Try moving it around a little.
My Gear:
Dean Cadillac
Gibson SG
Custom-made V

Randall RM100M

Boss TU2 Tuner
Jim Dunlop Zakk Wylde Sig. Crybaby Wah
Digitech "The Weapon"
Boss DD20 Giga Delay
Digitech Synth Wah
Digitech Whammy