If you have high Iso noise reduction on your camera, this could be the cause.
When you take the photograph with a high iso, the camera then takes another photo to see where the noise is, it then applies noise reduction to this (yes even with a raw file) and you get a reduced noise image.
The downside of this is sharpness, you lose some of it. Another downside is that it's not infallible. The hot pixels are possibly a result of the noise reduction in camera, I know Canon tend to reduce noise automatically with every Iso, hence the creamy skin! normally it's pretty undetectable but when it has to work hard, low light, high Iso it can and generally does fail.
If you can turn off the High Iso noise reduction, I would.
I know you can with Nikon, not too sure about Canon, perhaps someone with a Canon could enlighten us with a menu setting please?
By the way, if you are using CS3 Adobe Camera Raw to process your files, then there is a healing tool you can use to get rid of spots and the like.
Open all of the files in ACR and select all. Use the spot healing tool one the first one and if you have all of the other photos selected then it will automatically apply to every one.
I use this with dust spots on the sensor, it just magic's them away with out all of the huffle in photoshop

Hope this helps