I'm sorry for the long message. I really want to avoid having to bring
a 'pro' to check this out, so I want to exhaust my capabilities before
I have to shell out lots of cash:

The whole second floor of my house is frigid. I have a oil based boiler
(replaced new in late 2004), and the system is water based (hot water
flows into the radiators in the house). It has two zones, the first
floor and the second floor, controlled by separate thermostats.

Problems started a few weeks ago. Temperature was erratic upstairs.
Sometimes we'd set the thermostat to off and upstairs would be boiling.
Other times the thermostat would be high and heat would be
non-existant. Most of the time it worked fine. We still had the
thermostats from the older boiler (20 y/o at least) and after tinkering
w/ the temperature one day the front plate fell out (w/ the thermometer
coil) and heating stopped on the 2nd floor altoghether. I replaced the
thermostat w/ a nice new digital one (24V compatible w/ my unit), and
connected the R and W wires just as they were identified in the
original thermostat. Heat never came back to the 2nd floor.

The boiler is in the basement. (As my install guy explaned it) the
heating water coming out the front pipe, splitting into two, and one
going to the first floor zone, the other going to the second floor
zone. After the water makes it's way around, two pipes come back down
to the basement, each with a small pump. These pumps are hooked up to
the box that also connects the cables from the thermostats. The pipes
after the pumps join into one pipe and go back into the system. This is
the loop of warm water. Touching the pumps they are both running.

I noticed the back pipe coming down from the second floor was cold,
while the one coming down from the first floor was hot. I took this to
mean that the hot water wasn't making it's way around the system. I
'bled' the system to get rid of air in the 2nd floor zone (you could
feel air being forced out the pipes while it was being 'bled'). Now
both pipes are warm, which is good... but no heat upstairs yet!

Tracing the front pipe that pushes water from the boiler into the
upstairs rooms, I find that it starts off scolding hot, and the first
floor section is scolding hot all the way till the pipe leaves the
basement. Following the split for the second floor, it is hot
initially, but as I move farther away from the split it gets cold (even
before it leaves the basement).

What the heck could be going on? Could it be the thermostat causing
issues still? Tomorrow I'm going to pick up a voltage meter and make
sure the connections are good. Apart from that, what else could be
going wrong? I was quite surprised that the 2nd floor front pipes were
cold, given that the corresponding pipes at the end of the loop (w/ the
pumps) were warm. I made sure my installation guy explained everything
to me. Could I be misunderstanding how the system works? How could
there seemingly not be any hot water going up to the second floor, but
the pipe at the end of the loop is warm? Is the loop flowing the other
way instead (pumped up the back?)? The manual for the unit is useless.

Ok... that's about it. I'll be eternally greatful for whatever guidance
you can give me.