Has this happened to anyone else?

I loved the sound of my guitar after I discovered Elixir acoustic 10's, so much so that I got a full Anthem system fitted.
(I wanted to be able to easily put the great sound into my computer for recording)

Even before I plugged it in I straight away noticed a loss of bottom end. I assumed that the guitar shop had not fitted the strings that I asked for. A few months later I have put my trusty Elixir 10's back on, and the tone is just as bad.

Am I going mad?
Does the under saddle pickup kill bottom end tone?

And, what are my options?
Do I have to spend time & money looking for a new set of strings that sound good?

(It does sound great when plugged in with some light effects, but its not the same)

Help please