Firstly - IR is next to useless to read Copper - Coppers emissivity is even worse than Aluminium. The temp you think you are reading is not the actual temp. Read http://support.fluke.com/raytek-sales/D … EVB_LR.PDF to understand Non-Contact IR Temp measurement of Metals and Glass etc. There is a shedload more to it than point an IR gun and go 'thats the temp' .
Aluminium is 0.05 and is considered inaccurate - Polished Copper is a lowly 0.02!
Don't take my word for it - Ask Fluke! 
http://www.emlab.com/m/store/Fluke%20Th … Values.pdf
As to if you need to change - Probably easier to just ask the source code rather than guess. But the two thermistor types have very different Beta values - The QU-BD is 3950, the most common type of EPCOS 100k used has a beta of 4036. Beta value does effect temp greatly, and a quick look at the thermistor tables shows the differences:
QU-BD Thermistor Table
#if (THERMISTORHEATER_0 == 80) || (THERMISTORHEATER_1 == 80) || (THERMISTORHEATER_2 == 80) || (THERMISTORBED == 80) // QU-BD silicone bed QWG-104F-3950 thermistor
const short temptable_80[][2] PROGMEM = {
{1*OVERSAMPLENR, 938},
{31*OVERSAMPLENR, 314},
{41*OVERSAMPLENR, 290},
{51*OVERSAMPLENR, 272},
{61*OVERSAMPLENR, 258},
{71*OVERSAMPLENR, 247},
{81*OVERSAMPLENR, 237},
{91*OVERSAMPLENR, 229},
{101*OVERSAMPLENR, 221},
{111*OVERSAMPLENR, 215},
{121*OVERSAMPLENR, 209},
{131*OVERSAMPLENR, 204},
{141*OVERSAMPLENR, 199},
{151*OVERSAMPLENR, 195},
{161*OVERSAMPLENR, 190},
{171*OVERSAMPLENR, 187},
{181*OVERSAMPLENR, 183},
{191*OVERSAMPLENR, 179},
{201*OVERSAMPLENR, 176},
{221*OVERSAMPLENR, 170},
{241*OVERSAMPLENR, 165},
{261*OVERSAMPLENR, 160},
{281*OVERSAMPLENR, 155},
{301*OVERSAMPLENR, 150},
{331*OVERSAMPLENR, 144},
{361*OVERSAMPLENR, 139},
{391*OVERSAMPLENR, 133},
{421*OVERSAMPLENR, 128},
{451*OVERSAMPLENR, 123},
{491*OVERSAMPLENR, 117},
{531*OVERSAMPLENR, 111},
{571*OVERSAMPLENR, 105},
{611*OVERSAMPLENR, 100},
{641*OVERSAMPLENR, 95},
{681*OVERSAMPLENR, 90},
{711*OVERSAMPLENR, 85},
{751*OVERSAMPLENR, 79},
{791*OVERSAMPLENR, 72},
{811*OVERSAMPLENR, 69},
{831*OVERSAMPLENR, 65},
{871*OVERSAMPLENR, 57},
{881*OVERSAMPLENR, 55},
{901*OVERSAMPLENR, 51},
{921*OVERSAMPLENR, 45},
{941*OVERSAMPLENR, 39},
{971*OVERSAMPLENR, 28},
{981*OVERSAMPLENR, 23},
{991*OVERSAMPLENR, 17},
{1001*OVERSAMPLENR, 9},
{1021*OVERSAMPLENR, -27}
};
#endif
//{SD Patch} End
Type 1 Table:
#if (THERMISTORHEATER_0 == 1) || (THERMISTORHEATER_1 == 1) || (THERMISTORHEATER_2 == 1) || (THERMISTORBED == 1) //100k bed thermistor
const short temptable_1[][2] PROGMEM = {
{ 23*OVERSAMPLENR , 300 },
{ 25*OVERSAMPLENR , 295 },
{ 27*OVERSAMPLENR , 290 },
{ 28*OVERSAMPLENR , 285 },
{ 31*OVERSAMPLENR , 280 },
{ 33*OVERSAMPLENR , 275 },
{ 35*OVERSAMPLENR , 270 },
{ 38*OVERSAMPLENR , 265 },
{ 41*OVERSAMPLENR , 260 },
{ 44*OVERSAMPLENR , 255 },
{ 48*OVERSAMPLENR , 250 },
{ 52*OVERSAMPLENR , 245 },
{ 56*OVERSAMPLENR , 240 },
{ 61*OVERSAMPLENR , 235 },
{ 66*OVERSAMPLENR , 230 },
{ 71*OVERSAMPLENR , 225 },
{ 78*OVERSAMPLENR , 220 },
{ 84*OVERSAMPLENR , 215 },
{ 92*OVERSAMPLENR , 210 },
{ 100*OVERSAMPLENR , 205 },
{ 109*OVERSAMPLENR , 200 },
{ 120*OVERSAMPLENR , 195 },
{ 131*OVERSAMPLENR , 190 },
{ 143*OVERSAMPLENR , 185 },
{ 156*OVERSAMPLENR , 180 },
{ 171*OVERSAMPLENR , 175 },
{ 187*OVERSAMPLENR , 170 },
{ 205*OVERSAMPLENR , 165 },
{ 224*OVERSAMPLENR , 160 },
{ 245*OVERSAMPLENR , 155 },
{ 268*OVERSAMPLENR , 150 },
{ 293*OVERSAMPLENR , 145 },
{ 320*OVERSAMPLENR , 140 },
{ 348*OVERSAMPLENR , 135 },
{ 379*OVERSAMPLENR , 130 },
{ 411*OVERSAMPLENR , 125 },
{ 445*OVERSAMPLENR , 120 },
{ 480*OVERSAMPLENR , 115 },
{ 516*OVERSAMPLENR , 110 },
{ 553*OVERSAMPLENR , 105 },
{ 591*OVERSAMPLENR , 100 },
{ 628*OVERSAMPLENR , 95 },
{ 665*OVERSAMPLENR , 90 },
{ 702*OVERSAMPLENR , 85 },
{ 737*OVERSAMPLENR , 80 },
{ 770*OVERSAMPLENR , 75 },
{ 801*OVERSAMPLENR , 70 },
{ 830*OVERSAMPLENR , 65 },
{ 857*OVERSAMPLENR , 60 },
{ 881*OVERSAMPLENR , 55 },
{ 903*OVERSAMPLENR , 50 },
{ 922*OVERSAMPLENR , 45 },
{ 939*OVERSAMPLENR , 40 },
{ 954*OVERSAMPLENR , 35 },
{ 966*OVERSAMPLENR , 30 },
{ 977*OVERSAMPLENR , 25 },
{ 985*OVERSAMPLENR , 20 },
{ 993*OVERSAMPLENR , 15 },
{ 999*OVERSAMPLENR , 10 },
{ 1004*OVERSAMPLENR , 5 },
{ 1008*OVERSAMPLENR , 0 } //safety
};
#endif
The two thermistor tables look different to me - Close enough if you don't care for accuracy... there is a delta of up to 10°C in places...
But if you want accuracy - you really do need to change them. Regardless what your IR temp says
- so its either the comport is off or its the speed issue I mentioned above.