I just tested with a ToneCore Otto Filter here in the office. There should not be a big "gain" discrepancy between direct/bypassed tone and effected tone.

You should try removing the 2 hex-screws on the side of the dock and gently depress the plastic lock tab to release the module portion of the pedal. Take a look at the contact points (metal pins). Clean them if necessary and re-seat the module.

Re-test. If the symptoms still linger, the only way to really determine if the problem is originating in the module or the dock is by taking your module out and inserting it into a different dock. I've had users take a trip to the local Guitar Center's (Long & McQuade or Steve's Music for you, since I see you're writing us from Canada) Accessories department with the module and ask sales reps if it's OK to test the module with a new ToneCore dock in inventory. If you find that the effected signal in a different dock is still overpowering or underpowered, the issue is your module. If a new dock corrects the issue, you have your answer.