This is almost certainly your server or database... we run Feng 3.x and our db is currently 8GB and it is very quick to respond. We run with 8GB of RAM (although you really don't need this much for FO operations - this helps when we mysqldump our db for backups, though), SSD drives, and with some caching optimization.
The database is MySQL on the localhost, same with the other instances of Feng Office, however, just this 2 instance/project are crawling with the 12mb (size of DB) slower than the 15mb.
Newly created instances (for testing) have no problem (the no. of instances are now 7 from 5 previously) as well as the other ones.
BTW, instances, just to be clear are project sites. I may have called it differently than what you are accustomed to.
h t t p ://localhost/instance1
h t t p ://localhost/instance2
h t t p ://localhost/instance3
h t t p ://localhost/instance4
h t t p ://localhost/instance5
h t t p ://localhost/instance6
h t t p ://localhost/instance7