Keep in mind this items I discuss are currently "possibilities". The best find I have had in my career involved a 90% furnace that had 3 contractors that between them had basically rebuilt the furnace. New exchanger, draft motor, pressure switch, reroute of pvc etc. This furnace had literally every part except the outer cabinet replaced.
I went out and found the code of pressure switch (which the unit had done for 2 years).
I pulled the drains and even the collector box to examine the unit and noticed the water moved slow. I then, through research and taking a sample found that bacteria, spores or other organic matter was being drawn into the intake pipe, through the heating process and took up comfortable residence in the warm, wet environment inside the furnace and started to "jell" the condensate.
I then found that the company that made the furnace was aware of this, but had not received the right amount of complaints to qualify for a "technical release".
I installed a sanitary pan strip and at the request of the manufacturer a pice of copper tube in the collector box inside the furnace.
The copper creates a reaction that prohibits the growth of the micro-organisms.
The good news is the furnace never faulted again and the customer was relieved to find out he did not need to replace his furnace.
I am making this assumption based on your information of the quality and credibility of your contractor,and feel comfortable that they have addressed design, piping, mechanical or installation flaws. We already what is faulting....the issue now is to find why.
My theory of why it faults after sitting dormant for a while is the thickening of the condensate while sitting inactive.
I certainly hope you rectify your issue and I am available for any follow up questions you may have.