My guitar sounded a little thin, so I checked the spectrum analyzer and...

I mic'ed up my head through the cabinet in question, and through a different cabinet that I have. The difference was very obvious, it's definitely the cabinet. I'm gonna try to sell this one and buy a Harley Benton as soon as I can scrape up the cash.
 
Can you verify that you're using "speaker cable" to the cab? I don't think that it would make a great difference, at least on low volumes, but maybe you should check it out.
 
man it just looks like that because youre running the signal very low on volume and it's just showing the top of the frequency spectrum. Just for vizualization purposes try putting a limiter before the analyser and raise the gain until it is just tamming some peaks... give another look to the analyser and it should show the entire spectrum now. Cheers
 
I'd be more worried with those spikes at 750hz, 2500hz and 5khz. Content below 100hz... well generally speaking I'd say it's "space for bass" so if your tone is "thin" then I simply suggest you boost at 125hz or limit those spikes. A 4x12 cabinet resonance will be around 80hz so my guess would be that you didn't run your amp very loud. Am I right? This would lead to not having a whole lot of cabinet resonance. Or.. maybe you have a low cut filter somewhere in that chain.

And also I recommend using the IXL spectrum analyzer... just a personal preference though.