We have just had the same problem on an almost identical setup for the last month. This morning we tripped over http://tracker.firebirdsql.org/browse/CORE-5067 which is a problem in 2.5.4 relating to the security2.fdb sweep/OAT. 

I've just backed up and restored this file and all our problems melted away - long connection times dropped back down to lightning fast on both servers. 

We are planning on updating to 2.5.6 on these servers asap using mariadb ppa to jump the version from stock ubuntu.

Just thought I'd try to help fill in the grey area of your solution in case someone else is following in both our footsteps...if you don't think it was this feel free to say.

Ta

Ian