It totally shouldn't, but setting a custom white balance when shooting infrared makes a big difference on RAW captures.
I've taken two shots, one with tungsten white balance and one with a custom white balance, then processed them identically in ACR. The tungsten white balance produced a noticeably redder result. With the custom white balance it was (by my very rough estimate) 500 degrees cooler. This makes a big difference since I was developing IR at the very low end of ACR's temperature scale, around 2000 degrees. More importantly it impacts the relative saturation of colors (I'm guessing here) so that it is hard/impossible to even get the two to match at different temperatures.
Below are two recent samples shot using a custom white balance. Much different than my previous IR attempts.
(Anyone who can answer why it would matter for RAW captures, I'd like to know. It totally shouldn't make a difference.)
(Images are click-able for bigger size versions.)
Previous example, using tungsten white balance: