My furnace kicks on when it calls for hot water, but my registers do not heat up when it is needed for heat. The temperature can drop below what the thermostat is set at and it does not kick in. Although, when the hot water is running for a time (such as a shower), the registers will start to heat up but when the water is turned off they stop...

What kind of furnace? I assume forced air, but with a hot water coil.. Do you have hot water baseboards or radiators? What kind of thermostat? How long has the problem existed? Was anything done to the system recently? Your description of the system is too vague to do much with. Come back with more details.

Yes, please give us some more info. We will do our best to help, but we need to know exactly what we are trying to work on. My guess would be that you have a boiler that heats domestic hot water, and floor or baseboard hot water heat. Make and model of boiler, and pics of boiler and piping would help.

This sounds like a combination radiant heating/domestic potable water system that prioritizes recovery of the hot water supply, and something is wrong with the management controls. Probably not a DIY project.

Im siding with kc on this one, but please send the pics anyway, just in case it is something simple.

Here's a thought... does the system have more than one pump? If so, you may have a problem with the one responsible for radiant circulation.