Autocalibrate Probe settings not taking/setting right

Has anybody experienced a problem where they change tools in a program, and then insert an autocalibrate routine, but it doesn't follow the paramater sets that you have defined for that specific tool? So, this is a side problem to the program that I've been working on recently (if you want you can look at my history, but I don't think it really has anything to do with this problem, it might be a software problem), and I just can't figure it out. Basically, I just use 2 probes to inspect the part, and both of them have 2 separate calibrate parameter sets, but neither of them are uptaking the settings that I have specified in the dialog box. This is the first time that I have used auto-cal, so, I might have checked or unchecked something I wasn't supposed to, but I read over every single option in the probe calibration window and it's got me stumped. I'm sure somebody is going to tell me to rebuild the probe. :'( lolololololol. And...I get it. But one probe file has so many angles from other programs..... I might just create another probe file for this one program since the current one doesn't have tool changes in those other programs I mentioned before.