Worse Temp Variation with Am Standard and new Visionpro IAQ stat

[doob]

New Am Stand 80% 2 stage variable speed 100k gas furnace + Aprilaire 600 Hum installed to replace 54 yr old lennox 135K monster original to my 2 story 1954 cap cod house (1750sqft). At first the installers put in a single stage white rogers stat b/c they couldnt get the Am Std 2 stage stat to work. They left me with the board controling stages and i set it to just hold temp in the house at 66 F. Temp variation was good for this week(mid 30s outside temp) --only 3 F lower upstairs (5 supply and returns) except for the room over the garage which in past was 20 degrees cooler and now reached only 13 F or 53F max in that room.
I convinced the installer to put in a 2 stage stat like my contract said and finagled a visionpro IAQ. Now with the same outside temps, my variation is now higher at max 60 upstairs and 66 down. Why would this happen? My CPH for both stages is set at 5 and ive tried running the fan at contant as well but no change in temp. I even turned up the temp to 70 with NO change in upstairs temp! The only thing i can think thats different is that now my furnace only runs on low 1st stage usually for 9-12 mins whereas before it ran 9 mins low then 1 min on high before ramping down.
Ive air sealed all extensively; added R 50 in the attic 2 yrs ago and last week blew in insulation behind a big kneewall in the far room over the garage (90 sq ft wall with 8 inches cold airy space behind it heh) This room is now within 3 degrees to the other bedrooms.
Would changing the blower speed get me back within 3 degrees variation upstairs to downstairs? Dip switches 7 and 8 are set to ON so fan is always blowing at low. I asked my contractor if changing this to medium or going to higher CPH >5 would help me but they had no clue so I am asking the REAL pros here.

[mayguy]

What between the garage and bedroom floor?

Do you know where the ductwork is at for that room? Is is insulated or inside of a warm area?

How's the air flow in that vent up stairs?

I may change the CPH to 3 (longer run time)

[BaldLoonie]

Still sounds like a lot of furnace for a small house especially since you've insulated it like crazy.

But anyway, DIP switches 7 & 8 are heat speed. You have to turn the fan to constant at the thermostat which will run it at 1/2 of the cooling speed setting.

Even the best stat & furnace won't compensate for sizing issues or a poor duct system.

Sounds like you need more ducting to that room or an electric heater.

[doob]

What between the garage and bedroom floor?

Do you know where the ductwork is at for that room? Is is insulated or inside of a warm area?

How's the air flow in that vent up stairs?

I may change the CPH to 3 (longer run time)

Ductwork for this room runs thru wall adjoining garage and kitchen. I know theres lots of insulation in there but probably no air sealing. Supply Air flow is no different for any of the bedrooms though just lower than it is downstairs.
I know my ductwork is leaky--ive got the rectangular kind and can feel the seams leaking in the basement.
Insulation in the garage ceiling? heh. Theres one inch of batt insulation laying at the bottom of the joist space and on ceiling. Above that 1 inch theres approx 9 inches till you hit bedroom subfloor. Thats a job for next summer though.
Maybe i will lower the cph but i thought a higher one would eliminate temp vatiation despite shorter run times. Why would i lose 3 degrees in the other bedrooms when the only thing changed is the tstat? ducts furnace temps airflow all remained unchanged.

[doob]

Still sounds like a lot of furnace for a small house especially since you've insulated it like crazy.

But anyway, DIP switches 7 & 8 are heat speed. You have to turn the fan to constant at the thermostat which will run it at 1/2 of the cooling speed setting.

Even the best stat & furnace won't compensate for sizing issues or a poor duct system.

Sounds like you need more ducting to that room or an electric heater.

I thought it was alot too but did have manual J done with multiple quotes. Everytime i got a 74k heat loss. Cap cods are really hard to insulate: uninsulated and inaccessible kneewalls in all bedrooms, dormers, etc. I've even got this eyebrow roof running across the back btw 1st and 2nd floor which has no sheathing behind it allowing cold air to circ btw the floors. Downstairs ive got a porch converted to a 4 season sunroom on a slab really hoorible airsealing of the walls and windows but i did fix the floor there. In short despite all my work --R50 in attic, sill plate sealing, and sunroom floor; the house is still leaky.
Note I DO have a honeywell oil filled radiator in the far room since a yr ago works great but wanted to fix the room insulation and get my moneys worth out of my furnace by learning how best it should be set up. I can live with the 3 F difference in just that room for now but what im concerned about most is the general floor temp variation re upstairs vs downstairs when the 2 stage stat was added.. Why would i get worse variation?
Now about the fan--i am running it on constant and still have a 3 degree loss. Fan airflow ducts CPH temps all stayed same. Only the tstat was changed from single to 2 stage