What you are describing sounds quite possible- I personally haven't ever used an encoder without a quadrature decoder.

However...

The "OP" (does this stand for original post-guy?) isn't realizing too MANY pulses; he's realizing too FEW pulses - at least that's the way he describes it (which could be wrong).

We are trying to establish what his system "really" looks like so we can figure out where to go from here...

Since he's getting about 13k encoder pulses and sending about 23k motor pulses, my guessing includes the following:

1. His method for capturing pulses is bad (like he's missing a few cause he's polling for pulses instead of using hardware or something like that),

2. He's not really sending that many motor pulses (so he's fooling himself), or...

3. He really doesn't understand his system, like motor PPR, encoder PPR, gearing, dah, dah, dah...

I can't possibly speculate at this point WHY the difference exists without knowing WHAT the system really looks like - nor should I, as it might be misleading...