That particular furnace has a jumper on the control board to time on the second stage heating cycle. The jumper I believe will delay it 10 to 15 minutes. Furnace will run in low fire (1st stage) for a selected amount of time then kick up to high fire (2nd stage) after the selected delay. Now, if they jumpered the w1 and w2 terminals then the furnace will only run high fire and never low fire. (which is defeating the purpose of the two stage furnace). You need a new stat wire ran. Preferably an 8 conductor wire to ensure plenty of wires for almost any type of system. You can run the furnace with the control board's jumper and be ok since the 10 or 15 minute delay will usually suffice in maintaining your room temperature before high fire engages. Have them remove jumper from w1 and w2 and use the control boards jumper or run a new stat wire and hook it up properly. The extra stat wire is for turning on high fire only when needed.
Believe none of what you hear and half of what you see.