I have a pellet stove and hydro went and hooked generater up to it and then on the pellet stove the comp board came up with inverted polarity but fan ran fine and the blower was fine so I am confused so what does this mean

Just curious, are you a FDNY "CanMan"?

Inverted polarity means that the White, Neutral conductor, is more than likely connected incorrectly.

It is possible that the black and white conductors were reversed when installed. This needs to be corrected.