I was unable to determine the function of these settings. My system is running LV 5.1.1 on Windows 2000. I suspect some of these are particular to other platforms.

If anyone can give meaning to any of these settings, please let me know.

Setting Comments
activeX.freeThreaded  
AutoReInitSelectFeatureEnabled Setting this to True adds "Auto Reinitialization" to the case structure popup menu. Selecting this menu item changes the border of the case, but what it really does is a mystery.
AutoReInitSelectIsDefault Setting this to True causes new case structures to have above setting enabled by default.
cfm68kCallBack Mac only
compactWhileRunning  
coopLevel Mac?
flushDrawing  
fullKeyboardNav  
independentImageDepth  
initMemSize  
messyFileMutate  
paintPixmap  
print.xprOptions  
quietAppBuild A guess is that setting this to True will suppress the success message after an application has been successfully built, but it doesn't appear to work for LV 5.1.1.
RunAutotests Setting this to True adds "Run autotests" to the File menu, but I was unable to determine what it does.

It has been suggested that this may start a certain set of VIs at specific locations inside the LabVIEW directory. It's possible that this would be a set of VIs which test a lot of the LabVIEW functionality and reports incorrect results somehow. This is most probably for the LabVIEW developers in house testing of any new version to make sure no VI functions are broken after a rebuild.

trackTimeout  
updateSubVICtrlsFromUseConsts  
useOCXLicensing I've been told that the Active X specification includes functions which allow to integrate license checking into OCX controls. A container apparently can ignore this interface to some extent and this is what this setting may control.
windowSize  
xxxxx  
ExecEngineSelectPrompt  
ExecEngineSelectPrompt.DAQ  
ExecEngineSelectPrompt.FPGA  
ExecEngineSelectPrompt.Network  
ExecEngineSelectPrompt.Simulator