Since all homes and systems are different it's really hard for us to help answer your question without seeing your system design, layout, etc. It sounds like you may want to contact a local tech in your area to diagnose your issue.
Since all we do is filters I can provide a little info that might help you out in regards to filtration and how it affects a system;
Fiberglass filters like the EZ Flow filters we carry were originally developed to protect your furnace and/or air conditioning system. They are not intended to significantly improve your indoor air quality however they are the least restrictive and allow air to travel more freely through your system. Pleated filters do both. They improve your indoor air quality by attracting and capturing allergy-aggravating microparticles, and help keep your furnace equipment clean. Air in your home is continually re-circulated through the filter, and is cleaned with each pass through the filter. Pleated filters can be slightly more restrictive but really this only becomes an issue when cheap "non-tested" pleated filters are used and/or they are not changed on a regular basis. Our pleated filters have undergone strict testing and have extremely low pressure drops (the measurement for how much airflow is lost when a filter is in place).
If you have any questions please let us know and we will do our very best to help you out.