I actually worked through a similar issue. Sometimes it helps to slow down and ask yourself, what is really going on here... First, you're essentially measuring temperature twice: once with your reprap equipment and again with your external test equipment. Who is right? are they both wrong? Who knows?
This is how the temperature stuff works on my set up; I use the same hot end as you do, so its a good guess that the thermistor is the same one. Its a bit complicated so bear with me here:
The one lead of the thermistor connects to ground and a A/D pin. That same A/D pin is tied high through a normal resistor. Check out "voltage divider" on wikipedia to get the idea.
The microcontroller then essentially measures voltage on that A/D pin. As the thermistor gets warmer, its resistance goes down in a not so linear, but predictable manner. (That's why you need a lookup table, precomputing these saves the trouble of doing over and over again in code).
The microcontroller measures the incoming voltage on that pin which is varied by the thermistor: more voltage gets dumped to ground the hotter the thermistor gets. The microcontroller reads a particular voltage actually gets a particular number based on how many "bits" your A/D is. My A/D converter is 12 bits, so, I read out between 0 and 4096. yours could be 10, so that's 2^10 or 1024. But wait there's more: its measures this with respect to a Voltage reference.... I noticed some wierdness with my Vref during prototyping, but if you have a proper board then you're probably OK here. Basically you end up with a conversion factor, something like volts per A/D readings. that being said, if your VREF is off, then this would definitely set your Temperature measurements off too.
Now the lookuptable is nice so you don't do needless repetitive arithmetic in your microcontroller. The beta value is used in an equation to estimate the predicted resistance of the thermistor at a particular temperature. So if you didn't generate your own table there's no place for the beta value. I didn't bugger with the beta much here because the datasheet on mouser had a nice predicted ratios.
Now you know the Resistor value at a particular temperature, and you've got a voltage divider and an equasion for that. One resistor stays the same while the other changes on temperature, so compute the resulting voltage using that equation on Wikipedia, for different values of temperature, say, every 10 degrees or so. Then use your A/D info to convert that voltage into A/D readings. now you should be able to go from temperature to A/D reading in one jump, no math in a look-up table.
Its even better to graph this out and you will see a nice stretch of temperatures that you'll be really accurate within, but not so accurate higher or lower, depending on the value you set for the OTHER resistor that ties the A/D pin high. Google Docs worked quite well for this.
Its a few jumps, but my dev board is reading temperature with in a few degrees of my external temperature readings. Enthusiastic because I learned several new things while figuring this out.