There are a few 'things' going on here that might explain why you're experiencing what you're experiencing. (And I may not cover all the 'bases' but these 'things' may get you thinking in the short term. Others will stop by and offer more insight, I hope ...)
1) When cool air is 'agressively' moved by, say, a fan, it will feel colder. This is because as the cool/cold air 'moves' across your skin, heat is removed from your skin. Hence, your body senses a change in temperatire ON THE SKIN. And when this is occuring, the body has to work that much harder to keep the skin warm.
2) Depending on the HVAC system, it might be pulling in air from the outside, the basement (or wherever), or via the Return Vents. Depending on the source, this might explain the added coldness. If the basement is unheated, or at a lower temp, or if the air is coming from outside, then you have your answer. But if the air is TRUELY recirculated air, then are your ducts insulated? It's possible that the air is cooling a bit as it passes through the ducts. The further away from the unit a vent is, the longer it will take for the air in it (and the duct) to warm.
3) Now, with the fan off, you're also wondering why the heat isn't making its way to the 2nd floor. So I have to ask, where is your fireplace in relation to the 'access' to the 2nd floor??? If the fireplace is at the BACK of the house, and the stairs are at the FRONT of the house, it will take an awful LONG time for 'natural convection' to heat the 2nd floor. In fact, it may not occur to the degree that you'll feel it. What you must do is use ceiling fans, and such, to move the air on the 1st floor. If there are rooms and wall and other obstructions that will 'hinder' the TOTALLY FREE movement of air from one room to the next, that's another contributor to the poor distribution.
Consider this - Consider opening up a vent or 2 in the room(s) ABOVE the room where the fireplace is. This will help the warm air to rise up and out of the downstairs. My parents did this in their bedroom. It was directly over the living room in which the Franklin Stove sat. The vent was a straight vent. There wasn't any louvers or fans built into it. You'll have to 'box-out' the opening and finish it off but it's really easy to do. At the same time, they cut an opening in the wall next to the Stove so the Stove's blower could 'push' the hot air into the dining room and kitchen. My Father boxed that out and finished it off real nice. I don't want to say it looked a little silly but it was 'different'. At the same time, no one was cold in the kitchen (which was 2 rooms away from the Stove!) Which brings to mind - If your current stove DOESN'T have blowers on it, consider getting them in your next unit.
I'm sure there are other contributing factors to the coldness up stairs (including 'leaks') but they escape me. Stick around - Others should follow. My best to ya and hope this helps.
Jay J -Moderator
PS: Remember - Warm/Hot air rises. If there's anything you can do to 'move' it around (except via your HVAC fan), do that ...