Try added a small object and deleting it and see if the base updates the correct total. I noticed the totals lag a little. Also verify you didn't lose any members as a loss under 15 members can effect your totals.
ArchRex Dojhrom x ?
* Sidus Loricatus: B-NRG2, S-BS/Reg, T-Fire/Ice, MM-Bots/FF, St-NRG2, Dom-Psi/NRG, Cor-Son/Traps, Cor-Ice/Kin, Ctrl-Fire/Kin, PB-LB/LA
* Arachnos Loricatus: Soldier, Widow
* Praetoria Loricatus: B-DP/Dev, Cor-Elec/Elec
Have you previously added anything to your base? The figure on the SG page indicates TOTAL prestige, including the value of anything installed in your base. The figure on the editing screen indicates your 'balance available to spend'.
Paragon City Search And Rescue
The Mentor Project
The balance on my SG info screen goes up and down as I buy/sell stuff, but the total on my Edit screen is off it seems. I did delete a room earlier, so maybe it's just lag in the system. Dang banking hours...
Oops, that's right. The figure on the SG info screen is the amount available to spend. It's the figure at the SG Registrar that represents the total including base value. Must be lag in my brain... 
Paragon City Search And Rescue
The Mentor Project
it has happened to me all the time.
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This has been a persistant problem. I usually run into it when doing alot of editing, but it has happened when I made minor changes too.
I have had to log out, and log back in to get it to correct. (Out and in to the Game).
It's a Bug that perhaps never will be fixed....
Black-Strike: lvl 50 AR/Dark Corruptor
Brutally Beautiful: lvl 50 BA/Inv Brute
Seared Earth: lvl 50 EC/EA Dominator
Yashi Onuku: lvl 50 Ninja Blade/Ninjitsu Stalker
Death-Widow: lvl 50 Night Widow
When I look at my Super Group ID, I see that we have about 34k prestige, but when I am in the Base Editor it says I have 400. Is there some mechanic I don't know of, that sets aside prestige for something?