Low Output Level

 I cannot think of anything offhand that would cause this, and sounds like you are hearing different levels from simply tracking to playback (I am not sure I understand the OP fully). Is there a difference between your track's metering levels while recording and playback for that track?
 
I am not familiar with your audio interface, so wondering if there is routing going on there (external to FX inside SONAR) that are contributing.

ampfixer
 
The same thing seems to happen when exporting audio. I have to run all the levels high on export or the output file will be too quiet.
 
I'll have to figure out if the routing is at play.

I don't understand this. When you export, I assume you adjust the peak level of the master bus to something feasible, say, between -6 dB and -0,3 dB, depending on what the purpose is. Those levels represent the normal, usable levels, and you can not go any louder than that by "running the levels high". That is then the level of the audio file no matter what gear you use for the playback. The position of the volume knob is another thing, it has nothing to do with the loudness.
 
If it's a mix the RMS level of which you've taken care of, that level is the true loudness of the file played back anywhere. No other play back gear makes it any louder than that, unless compressors or such are in the playback chain.
 
When you have experienced these "low level files", you surely have checked their levels? What have they been like?
Your "swearing the levels must have been low" doesn't tell anything. How were the digits?
 
There must be something very basic causing this phenomenon.