#5
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".
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#6
It could be the position of the speaker thats emphasising certain frequencies. Try moving it around a little.
My Gear:
Guitars:
Dean Cadillac
Gibson SG
Custom-made V

Amp:
Randall RM100M

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